diff --git a/README.md b/README.md index f889883f..30e80a2b 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![pylint](imgs/pylint.svg)](https://github.com/acenglish/truvari/actions/workflows/pylint.yml) [![FuncTests](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml/badge.svg?branch=develop&event=push)](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml) [![coverage](imgs/coverage.svg)](https://github.com/acenglish/truvari/actions/workflows/func_tests.yml) -[![develop](https://img.shields.io/github/commits-since/acenglish/truvari/v5.0.0)](https://github.com/ACEnglish/truvari/compare/v5.0.0...develop) +[![develop](https://img.shields.io/github/commits-since/acenglish/truvari/v5.1.1)](https://github.com/ACEnglish/truvari/compare/v5.1.1...develop) [![Downloads](https://static.pepy.tech/badge/truvari)](https://pepy.tech/project/truvari) ![Logo](https://raw.githubusercontent.com/ACEnglish/truvari/develop/imgs/BoxScale1_DarkBG.png) @@ -26,12 +26,12 @@ Each sub-command contains help documentation. Start with `truvari -h` to see ava The current most common Truvari use case is for structural variation benchmarking: ``` - truvari bench -b base.vcf.gz -c comp.vcf.gz -o output_dir/ + truvari bench -b base.vcf.gz -c comp.vcf.gz -f reference.fa -o output_dir/ ``` Find more matches by harmonizing phased varians using refine: ``` - truvari refine -R -U -r reference.fa --regions output_dir/candidate.refine.bed output_dir/ + truvari refine output_dir/ ``` Use Truvari's comparison engine to consolidate redundant variants in a merged multi-sample VCF: diff --git a/imgs/coverage.svg b/imgs/coverage.svg index ea71b13a..6a91c8d4 100644 --- a/imgs/coverage.svg +++ b/imgs/coverage.svg @@ -17,7 +17,7 @@ coverage - 90% - 90% + 91% + 91% diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz index 8119b19e..90a954c5 100644 Binary files a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz and 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b/repo_utils/answer_key/ga4gh/ga4gh_withrefine_orig.comp.vcf.gz.tbi index a55580c5..f296c8fd 100644 Binary files a/repo_utils/answer_key/ga4gh/ga4gh_withrefine_orig.comp.vcf.gz.tbi and b/repo_utils/answer_key/ga4gh/ga4gh_withrefine_orig.comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/help.txt b/repo_utils/answer_key/help.txt index 0fdc9aed..ba1f8fab 100644 --- a/repo_utils/answer_key/help.txt +++ b/repo_utils/answer_key/help.txt @@ -1,6 +1,6 @@ usage: truvari [-h] CMD ... -Truvari v5.1.1 Structural Variant Benchmarking and Annotation +Truvari v5.2.0 Structural Variant Benchmarking and Annotation Available commands: bench Performance metrics from comparison of two VCFs diff --git a/repo_utils/answer_key/refine/refine_output_one/log.txt b/repo_utils/answer_key/refine/refine_output_one/log.txt index a1575de6..6b5b5d4a 100644 --- a/repo_utils/answer_key/refine/refine_output_one/log.txt +++ b/repo_utils/answer_key/refine/refine_output_one/log.txt @@ -1,6 +1,6 @@ -2025-02-02 06:13:45,675 [INFO] Truvari v5.0.1.dev0+aef4e1a.uc -2025-02-02 06:13:45,675 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_one -2025-02-02 06:13:45,676 [INFO] Params: +2025-02-16 01:48:20,256 [INFO] Truvari v5.1.1 +2025-02-16 01:48:20,257 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_one +2025-02-16 01:48:20,258 [INFO] Params: { "base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", @@ -36,10 +36,10 @@ "skip_gt": false, "max_resolve": 25000 } -2025-02-02 06:13:45,720 [INFO] Including 225 bed regions -2025-02-02 06:13:49,217 [INFO] Zipped 7157 variants Counter({'comp': 5302, 'base': 1855}) -2025-02-02 06:13:49,218 [INFO] 211 chunks of 7157 variants Counter({'__filtered': 6137, 'base': 569, 'comp': 451}) -2025-02-02 06:13:49,324 [INFO] Stats: { +2025-02-16 01:48:20,308 [INFO] Including 225 bed regions +2025-02-16 01:48:24,069 [INFO] Zipped 7157 variants Counter({'comp': 5302, 'base': 1855}) +2025-02-16 01:48:24,070 [INFO] 211 chunks of 7157 variants Counter({'__filtered': 6137, 'base': 569, 'comp': 451}) +2025-02-16 01:48:24,192 [INFO] Stats: { "TP-base": 387, "TP-comp": 387, "FP": 64, @@ -71,4 +71,4 @@ } } } -2025-02-02 06:13:49,324 [INFO] Finished bench +2025-02-16 01:48:24,193 [INFO] Finished bench diff --git a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz index 3248eb1a..8414eeeb 100644 Binary files a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz and b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi index 204e68a7..ee451757 100644 Binary files a/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_one/phab.output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed b/repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed index 9829ca0b..0d5c82f1 100644 --- a/repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed +++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed @@ -1,5 +1,5 @@ chr20 5040466 5040487 -chr20 5041931 5042443 +chr20 5041952 5042292 chr20 16257844 16259455 chr20 32723034 32723055 chr20 51953809 51953830 \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz index 1425844e..0c46021c 100644 Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi index 81d42591..3d6ce09d 100644 Binary files a/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_one/phab_bench/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json b/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json index fa33cbbc..c2c7443f 100644 --- a/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json +++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json @@ -1 +1 @@ -{"base": "test_results/refine_output_one/phab.output.vcf.gz", "comp": "test_results/refine_output_one/phab.output.vcf.gz", "output": "test_results/refine_output_one/phab_bench", "includebed": "/tmp/xn9atc8u.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "bnddist": 100, "sizemin": 5, "sizefilt": 5, "sizemax": -1, "passonly": false, "no_ref": "a", "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": true, "short_circuit": true, "skip_gt": false, "max_resolve": 25000} \ No newline at end of file +{"base": "test_results/refine_output_one/phab.output.vcf.gz", "comp": "test_results/refine_output_one/phab.output.vcf.gz", "output": "test_results/refine_output_one/phab_bench", "includebed": "/tmp/_0inhoz1.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "bnddist": 100, "sizemin": 5, "sizefilt": 5, "sizemax": -1, "passonly": false, "no_ref": "a", "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": true, "short_circuit": true, "skip_gt": false, "max_resolve": 25000} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json b/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json index 311c8cab..8ae78e96 100644 --- a/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json +++ b/repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json @@ -1,27 +1,27 @@ { - "TP-base": 361, - "TP-comp": 361, - "FP": 5, + "TP-base": 320, + "TP-comp": 320, + "FP": 9, "FN": 2, - "precision": 0.9863387978142076, - "recall": 0.9944903581267218, - "f1": 0.9903978052126201, - "base cnt": 363, - "comp cnt": 366, - "TP-comp_TP-gt": 361, + "precision": 0.9726443768996961, + "recall": 0.9937888198757764, + "f1": 0.9831029185867896, + "base cnt": 322, + "comp cnt": 329, + "TP-comp_TP-gt": 320, "TP-comp_FP-gt": 0, - "TP-base_TP-gt": 361, + "TP-base_TP-gt": 320, "TP-base_FP-gt": 0, "gt_concordance": 1.0, "gt_matrix": { "(0, 1)": { - "(1, 0)": 136 + "(1, 0)": 125 }, "(1, 0)": { - "(0, 1)": 178 + "(0, 1)": 162 }, "(1, 1)": { - "(1, 1)": 47 + "(1, 1)": 33 } } } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/phab_bench/tp-base.vcf.gz index 1c63aba8..d28a65b0 100644 Binary files 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a/repo_utils/answer_key/refine/refine_output_one/refine.comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_one/refine.comp.vcf.gz index 614745db..36e209e0 100644 Binary files a/repo_utils/answer_key/refine/refine_output_one/refine.comp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_one/refine.comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_one/refine.comp.vcf.gz.tbi index 91810b2b..941b7455 100644 Binary files a/repo_utils/answer_key/refine/refine_output_one/refine.comp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_one/refine.comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.log.txt b/repo_utils/answer_key/refine/refine_output_one/refine.log.txt index 5bdcf598..4d8ea5f1 100644 --- a/repo_utils/answer_key/refine/refine_output_one/refine.log.txt +++ b/repo_utils/answer_key/refine/refine_output_one/refine.log.txt @@ -1,9 +1,9 @@ -2025-02-02 06:13:50,924 [INFO] Truvari v5.0.1.dev0+aef4e1a.uc -2025-02-02 06:13:50,924 [INFO] Command /data/truvari/__main__.py refine --write-phab --coords O --buffer 100 --use-original-vcfs -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_one -2025-02-02 06:13:50,925 [INFO] Params: +2025-02-16 01:48:25,954 [INFO] Truvari v5.1.1 +2025-02-16 01:48:25,954 [INFO] Command /data/truvari/__main__.py refine --write-phab --coords O --use-original-vcfs -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_one +2025-02-16 01:48:25,956 [INFO] Params: { "benchdir": "test_results/refine_output_one", - "align": "mafft", + "align": "poa", "use_original_vcfs": true, "write_phab": true, "threads": 4, @@ -15,19 +15,30 @@ "mafft_params": "--auto --thread 1", "debug": false } -2025-02-02 06:13:50,925 [INFO] Setting up regions -2025-02-02 06:13:50,941 [INFO] Evaluating 225 regions -2025-02-02 06:13:50,942 [INFO] Extending the regions by 100 bases -2025-02-02 06:13:50,979 [INFO] Found 1 chromosomes with overlapping regions -2025-02-02 06:13:51,987 [INFO] 75 regions to be refined -2025-02-02 06:13:51,997 [WARNING] Harmonizing variants ≥50kbp is not recommended -2025-02-02 06:13:51,998 [INFO] Preparing regions -2025-02-02 06:13:52,006 [INFO] Extracting haplotypes -2025-02-02 06:13:53,095 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:888: CoverageWarning:No data was collected. (no-data-collected) -2025-02-02 06:13:53,099 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:888: CoverageWarning:No data was collected. (no-data-collected) -2025-02-02 06:13:53,110 [INFO] Harmonizing variants -2025-02-02 06:13:55,109 [INFO] Running bench -2025-02-02 06:13:55,134 [INFO] Including 75 bed regions -2025-02-02 06:13:57,321 [INFO] Zipped 4134 variants Counter({'base': 2067, 'comp': 2067}) -2025-02-02 06:13:57,322 [INFO] 76 chunks of 4134 variants Counter({'__filtered': 3405, 'comp': 366, 'base': 363}) -2025-02-02 06:13:58,488 [INFO] Finished refine +2025-02-16 01:48:25,956 [INFO] Setting up regions +2025-02-16 01:48:25,970 [INFO] Evaluating 225 regions +2025-02-16 01:48:25,971 [INFO] Extending the regions by 100 bases +2025-02-16 01:48:26,011 [INFO] Found 1 chromosomes with overlapping regions +2025-02-16 01:48:27,023 [INFO] 75 regions to be refined +2025-02-16 01:48:27,034 [WARNING] Harmonizing variants ≥50kbp is not recommended +2025-02-16 01:48:27,035 [INFO] Preparing regions +2025-02-16 01:48:27,043 [INFO] Extracting haplotypes +2025-02-16 01:48:28,113 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:892: CoverageWarning:No data was collected. (no-data-collected) +2025-02-16 01:48:28,116 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:892: CoverageWarning:No data was collected. (no-data-collected) +2025-02-16 01:48:28,130 [INFO] Harmonizing variants +2025-02-16 01:48:30,259 [INFO] Running bench +2025-02-16 01:48:30,288 [INFO] Including 75 bed regions +2025-02-16 01:48:32,225 [INFO] Zipped 4226 variants Counter({'base': 2113, 'comp': 2113}) +2025-02-16 01:48:32,226 [INFO] 77 chunks of 4226 variants Counter({'__filtered': 3575, 'comp': 329, 'base': 322}) +2025-02-16 01:48:33,331 [INFO] Stats: { + "TP-base": 555, + "TP-comp": 555, + "FP": 20, + "FN": 2, + "precision": 0.9652173913043478, + "recall": 0.9964093357271095, + "f1": 0.980565371024735, + "base cnt": 557, + "comp cnt": 575 +} +2025-02-16 01:48:33,332 [INFO] Finished refine diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt index 20e3349f..3079a412 100644 --- a/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt +++ b/repo_utils/answer_key/refine/refine_output_one/refine.regions.txt @@ -1,36 +1,36 @@ chrom start end in_tpbase in_tp in_fn in_fp refined out_tpbase out_tp out_fn out_fp state -chr20 278800 279286 3 3 1 0 True 5 5 0 0 TP +chr20 278800 279286 3 3 1 0 True 4 4 0 0 TP chr20 420455 420870 2 2 0 0 False 2 2 0 0 TP -chr20 641736 642565 3 3 2 0 True 5 5 0 0 TP +chr20 641736 642565 3 3 2 0 True 3 3 0 0 TP chr20 709629 710075 2 2 0 0 False 2 2 0 0 TP chr20 1149707 1150320 2 2 0 0 False 2 2 0 0 TP chr20 1257833 1260628 2 2 0 0 False 2 2 0 0 TP chr20 1301499 1302767 2 2 0 0 False 2 2 0 0 TP -chr20 2240825 2241826 1 1 4 1 True 5 5 0 0 TP +chr20 2240825 2241826 1 1 4 1 True 4 4 0 0 TP chr20 2442866 2444043 2 2 0 0 False 2 2 0 0 TP chr20 2842474 2843097 2 2 0 0 False 2 2 0 0 TP -chr20 4032119 4033701 2 2 2 1 True 4 4 0 0 TP +chr20 4032119 4033701 2 2 2 1 True 2 2 0 0 TP chr20 4482485 4482834 2 2 0 0 False 2 2 0 0 TP chr20 4811059 4811329 1 1 0 0 False 1 1 0 0 TP chr20 4844638 4845006 2 2 0 0 False 2 2 0 0 TP chr20 5039849 5040599 0 0 0 2 True 0 0 0 2 FP -chr20 5041757 5042809 1 1 1 1 True 2 2 0 1 FP +chr20 5041757 5042809 1 1 1 1 True 2 2 0 5 FP chr20 5554004 5554285 0 0 0 0 False 0 0 0 0 TN chr20 5962227 5962510 0 0 0 0 False 0 0 0 0 TN chr20 7435115 7435849 2 2 0 0 False 2 2 0 0 TP chr20 7719230 7719514 1 1 0 0 False 1 1 0 0 TP chr20 7720811 7721419 1 1 0 0 False 1 1 0 0 TP -chr20 8661811 8662757 1 1 3 1 True 9 9 0 0 TP +chr20 8661811 8662757 1 1 3 1 True 5 5 0 0 TP chr20 9015448 9016139 1 1 0 0 False 1 1 0 0 TP chr20 9188345 9189662 2 2 0 0 False 2 2 0 0 TP chr20 10802576 10803058 1 1 1 0 True 2 2 0 0 TP chr20 10977697 10978077 2 2 0 0 False 2 2 0 0 TP chr20 13848064 13848749 3 3 1 0 True 3 3 0 0 TP chr20 14485571 14485848 0 0 0 0 False 0 0 0 0 TN -chr20 14861837 14862841 5 5 5 1 True 15 15 0 0 TP +chr20 14861837 14862841 5 5 5 1 True 12 12 0 0 TP chr20 16226854 16228587 3 3 0 0 False 3 3 0 0 TP chr20 16257641 16259445 2 2 2 0 True 4 4 1 1 FN,FP -chr20 16395049 16395521 3 3 1 0 True 3 3 0 0 TP +chr20 16395049 16395521 3 3 1 0 True 4 4 0 0 TP chr20 16894260 16894535 1 1 0 0 False 1 1 0 0 TP chr20 17081116 17081510 2 2 0 0 False 2 2 0 0 TP chr20 17197023 17197341 2 2 0 0 False 2 2 0 0 TP @@ -39,14 +39,14 @@ chr20 18208997 18210827 3 3 2 1 True 5 5 0 0 TP chr20 18675550 18676015 2 2 0 0 False 2 2 0 0 TP chr20 19080658 19080927 0 0 0 0 False 0 0 0 0 TN chr20 19663266 19663626 2 2 0 0 False 2 2 0 0 TP -chr20 20295855 20296665 2 2 2 1 True 3 3 0 0 TP +chr20 20295855 20296665 2 2 2 1 True 5 5 0 0 TP chr20 20320185 20320679 1 1 2 1 True 2 2 0 0 TP -chr20 20337100 20337807 1 1 6 2 True 3 3 0 0 TP -chr20 20354470 20358423 7 7 8 1 True 16 16 0 0 TP +chr20 20337100 20337807 1 1 6 2 True 9 9 0 0 TP +chr20 20354470 20358423 7 7 8 1 True 12 12 0 0 TP chr20 20458540 20459037 2 2 0 0 False 2 2 0 0 TP chr20 21120112 21120639 2 2 0 0 False 2 2 0 0 TP chr20 21721074 21721835 2 2 1 0 True 3 3 0 0 TP -chr20 22081861 22084222 4 4 3 1 True 9 9 0 0 TP +chr20 22081861 22084222 4 4 3 1 True 7 7 0 0 TP chr20 22471731 22472229 2 2 0 0 False 2 2 0 0 TP chr20 22882602 22882930 2 2 0 0 False 2 2 0 0 TP chr20 23155404 23156075 3 3 2 2 True 5 5 0 0 TP @@ -71,34 +71,34 @@ chr20 32724827 32725099 0 0 0 0 False 0 0 0 0 TN chr20 34205519 34206060 1 1 0 0 False 1 1 0 0 TP chr20 34235650 34236313 0 0 2 1 True 2 2 0 0 TP chr20 35539020 35539824 4 4 0 0 False 4 4 0 0 TP -chr20 35579913 35580986 1 1 2 1 True 7 7 0 0 TP +chr20 35579913 35580986 1 1 2 1 True 3 3 0 0 TP chr20 36642042 36642322 1 1 0 0 False 1 1 0 0 TP chr20 37361652 37362158 2 2 0 0 False 2 2 0 0 TP -chr20 38123490 38124805 2 2 1 4 True 7 7 0 0 TP +chr20 38123490 38124805 2 2 1 4 True 4 4 0 0 TP chr20 38194433 38194766 2 2 0 0 False 2 2 0 0 TP chr20 38313518 38315169 3 3 0 0 False 3 3 0 0 TP chr20 38462831 38464883 2 2 2 0 True 4 4 0 0 TP chr20 38895636 38896715 1 1 0 0 False 1 1 0 0 TP chr20 40982603 40983042 2 2 0 0 False 2 2 0 0 TP -chr20 41196110 41196748 3 3 1 0 True 4 4 0 0 TP +chr20 41196110 41196748 3 3 1 0 True 5 5 0 0 TP chr20 41257474 41258303 0 0 0 1 False 0 0 0 1 FP chr20 41278222 41278484 0 0 0 0 False 0 0 0 0 TN chr20 41278646 41278915 0 0 0 0 False 0 0 0 0 TN -chr20 44763796 44764385 2 2 1 0 True 2 2 0 0 TP -chr20 45600469 45600846 2 2 2 0 True 2 2 0 0 TP +chr20 44763796 44764385 2 2 1 0 True 3 3 0 0 TP +chr20 45600469 45600846 2 2 2 0 True 4 4 0 0 TP chr20 45773643 45774179 1 1 0 0 False 1 1 0 0 TP chr20 46788707 46789630 2 2 0 0 False 2 2 0 0 TP chr20 47225424 47225745 2 2 0 0 False 2 2 0 0 TP chr20 47894314 47899105 3 3 0 0 False 3 3 0 0 TP chr20 48390798 48391331 2 2 0 0 False 2 2 0 0 TP -chr20 48449605 48450561 4 4 2 0 True 6 6 0 0 TP +chr20 48449605 48450561 4 4 2 0 True 5 5 0 0 TP chr20 48811379 48811875 1 1 0 0 False 1 1 0 0 TP chr20 48959259 48959752 2 2 0 0 False 2 2 0 0 TP chr20 49834009 49834658 2 2 1 0 True 3 3 0 0 TP chr20 50258350 50258651 2 2 0 0 False 2 2 0 0 TP chr20 50300350 50301661 2 2 0 0 False 2 2 0 0 TP chr20 50666048 50666993 2 2 0 0 False 2 2 0 0 TP -chr20 50775444 50776123 1 1 2 1 True 4 4 0 0 TP +chr20 50775444 50776123 1 1 2 1 True 3 3 0 0 TP chr20 50853539 50854028 2 2 0 0 False 2 2 0 0 TP chr20 51060950 51061358 2 2 0 0 False 2 2 0 0 TP chr20 51500492 51500980 2 2 0 0 False 2 2 0 0 TP @@ -111,16 +111,16 @@ chr20 53415542 53415960 2 2 0 0 False 2 2 0 0 TP chr20 53912928 53913452 2 2 0 0 False 2 2 0 0 TP chr20 54690671 54690973 2 2 0 0 False 2 2 0 0 TP chr20 55532059 55533478 1 1 0 0 False 1 1 0 0 TP -chr20 55624382 55625907 6 6 6 0 True 11 11 0 0 TP -chr20 55627244 55628550 7 7 3 0 True 8 8 0 0 TP -chr20 55943819 55945907 2 2 2 1 True 5 5 0 0 TP -chr20 56280322 56282214 4 4 5 1 True 10 10 0 0 TP +chr20 55624382 55625907 6 6 6 0 True 14 14 0 0 TP +chr20 55627244 55628550 7 7 3 0 True 9 9 0 0 TP +chr20 55943819 55945907 2 2 2 1 True 4 4 0 0 TP +chr20 56280322 56282214 4 4 5 1 True 16 16 0 0 TP chr20 56284158 56284507 2 2 0 0 False 2 2 0 0 TP chr20 56710455 56711293 2 2 0 0 False 2 2 0 0 TP -chr20 57090572 57091511 1 1 2 0 True 4 4 0 0 TP +chr20 57090572 57091511 1 1 2 0 True 3 3 0 0 TP chr20 57110112 57110885 2 2 0 0 False 2 2 0 0 TP chr20 57189846 57190640 0 0 3 1 True 1 1 0 0 TP -chr20 57350708 57351087 1 1 1 0 True 3 3 0 0 TP +chr20 57350708 57351087 1 1 1 0 True 2 2 0 0 TP chr20 57417171 57418334 2 2 0 0 False 2 2 0 0 TP chr20 57780634 57781606 2 2 0 0 False 2 2 0 0 TP chr20 57948698 57949590 1 1 4 1 True 5 5 0 0 TP @@ -129,19 +129,19 @@ chr20 58196600 58197036 2 2 0 0 False 2 2 0 0 TP chr20 58309323 58309912 1 1 0 0 False 1 1 0 0 TP chr20 58519802 58520472 2 2 0 0 False 2 2 0 0 TP chr20 58694762 58695511 2 2 0 0 False 2 2 0 0 TP -chr20 59383704 59385335 3 3 2 0 True 4 4 0 0 TP +chr20 59383704 59385335 3 3 2 0 True 5 5 0 0 TP chr20 59441936 59442373 2 2 0 0 False 2 2 0 0 TP chr20 60087291 60088065 2 2 0 0 False 2 2 0 0 TP -chr20 60314230 60315120 2 2 2 0 True 5 5 0 0 TP +chr20 60314230 60315120 2 2 2 0 True 7 7 0 0 TP chr20 60600007 60600420 1 1 0 0 False 1 1 0 0 TP chr20 60702842 60703215 2 2 2 1 True 3 3 0 0 TP chr20 60763931 60764734 2 2 0 0 False 2 2 0 0 TP chr20 61045827 61046387 1 1 0 0 False 1 1 0 0 TP chr20 61100692 61102787 1 1 4 1 True 3 3 0 0 TP chr20 61176625 61177074 2 2 0 0 False 2 2 0 0 TP -chr20 61201583 61202574 2 2 4 1 True 7 7 0 0 TP +chr20 61201583 61202574 2 2 4 1 True 6 6 0 0 TP chr20 61229487 61229817 2 2 0 0 False 2 2 0 0 TP -chr20 61282406 61283769 4 4 2 0 True 6 6 0 0 TP +chr20 61282406 61283769 4 4 2 0 True 4 4 0 0 TP chr20 61289525 61290655 1 1 1 1 True 2 2 0 0 TP chr20 61329158 61329677 0 0 0 2 False 0 0 0 2 FP chr20 61331428 61331853 2 2 0 0 False 2 2 0 0 TP @@ -154,33 +154,33 @@ chr20 61723733 61724344 1 1 0 0 False 1 1 0 0 TP chr20 61744088 61744754 2 2 0 0 False 2 2 0 0 TP chr20 61783303 61784939 3 3 0 0 False 3 3 0 0 TP chr20 61919576 61921474 2 2 0 0 False 2 2 0 0 TP -chr20 62057473 62059239 1 1 3 1 True 7 7 0 0 TP +chr20 62057473 62059239 1 1 3 1 True 3 3 0 0 TP chr20 62212744 62213974 4 4 0 0 False 4 4 0 0 TP -chr20 62270179 62271194 1 1 3 1 True 4 4 0 0 TP +chr20 62270179 62271194 1 1 3 1 True 3 3 0 0 TP chr20 62317737 62318559 2 2 0 0 False 2 2 0 0 TP -chr20 62320931 62321973 2 2 3 0 True 5 5 0 0 TP -chr20 62349512 62350032 1 1 5 1 True 6 6 0 0 TP +chr20 62320931 62321973 2 2 3 0 True 6 6 0 0 TP +chr20 62349512 62350032 1 1 5 1 True 9 9 0 0 TP chr20 62360090 62360812 0 0 7 2 True 5 5 0 0 TP chr20 62417324 62418162 3 3 0 0 False 3 3 0 0 TP chr20 62422344 62422891 2 2 0 0 False 2 2 0 0 TP chr20 62504179 62504714 2 2 0 0 False 2 2 0 0 TP chr20 62622208 62622607 1 1 0 0 False 1 1 0 0 TP chr20 62824934 62825339 2 2 0 0 False 2 2 0 0 TP -chr20 62830512 62830938 2 2 1 1 True 2 2 0 0 TP +chr20 62830512 62830938 2 2 1 1 True 3 3 0 0 TP chr20 62875072 62875656 2 2 3 0 True 3 3 0 0 TP chr20 62975688 62976324 1 1 0 0 False 1 1 0 0 TP chr20 62986210 62986905 2 2 0 0 False 2 2 0 0 TP -chr20 63027897 63028266 2 2 1 0 True 4 4 0 0 TP +chr20 63027897 63028266 2 2 1 0 True 3 3 0 0 TP chr20 63028776 63029502 2 2 0 1 True 2 2 0 0 TP -chr20 63048933 63049512 3 3 1 0 True 2 2 0 0 TP +chr20 63048933 63049512 3 3 1 0 True 3 3 0 0 TP chr20 63068309 63068899 2 2 0 0 False 2 2 0 0 TP chr20 63103149 63103592 1 1 0 0 False 1 1 0 0 TP chr20 63154485 63155095 1 1 1 0 True 2 2 0 0 TP chr20 63156667 63157425 2 2 0 0 False 2 2 0 0 TP chr20 63158083 63158826 2 2 0 0 False 2 2 0 0 TP -chr20 63167287 63167727 2 2 1 0 True 3 3 0 0 TP +chr20 63167287 63167727 2 2 1 0 True 5 5 0 0 TP chr20 63220080 63220659 1 1 0 0 False 1 1 0 0 TP -chr20 63221380 63221976 1 1 2 1 True 2 2 0 0 TP +chr20 63221380 63221976 1 1 2 1 True 4 4 0 0 TP chr20 63226386 63226752 1 1 0 0 False 1 1 0 0 TP chr20 63234003 63234516 1 1 0 0 False 1 1 0 0 TP chr20 63235229 63235550 2 2 0 0 False 2 2 0 0 TP @@ -201,7 +201,7 @@ chr20 63553194 63553857 1 1 0 0 False 1 1 0 0 TP chr20 63559188 63560063 1 1 2 1 True 4 4 0 0 TP chr20 63641679 63642235 1 1 2 1 True 2 2 0 0 TP chr20 63669479 63670596 2 2 0 0 False 2 2 0 0 TP -chr20 63693225 63693984 1 1 6 1 True 10 10 0 0 TP +chr20 63693225 63693984 1 1 6 1 True 9 9 0 0 TP chr20 63731138 63731891 1 1 0 0 False 1 1 0 0 TP chr20 63747182 63747707 2 2 0 0 False 2 2 0 0 TP chr20 63770812 63771203 0 0 0 2 False 0 0 0 2 FP @@ -209,17 +209,17 @@ chr20 63793529 63793887 1 1 0 0 False 1 1 0 0 TP chr20 63824531 63825244 2 2 0 0 False 2 2 0 0 TP chr20 63853570 63854126 1 1 0 0 False 1 1 0 0 TP chr20 63879205 63880634 1 1 0 0 False 1 1 0 0 TP -chr20 63948414 63948858 2 2 1 1 True 3 3 0 0 TP -chr20 63964668 63966717 1 1 1 0 True 1 1 0 0 TP +chr20 63948414 63948858 2 2 1 1 True 2 2 0 0 TP +chr20 63964668 63966717 1 1 1 0 True 2 2 0 0 TP chr20 64011622 64013101 2 2 0 0 False 2 2 0 0 TP chr20 64042616 64043161 1 1 0 0 False 1 1 0 0 TP chr20 64065753 64066111 0 0 0 1 False 0 0 0 1 FP chr20 64090604 64091489 0 0 0 2 False 0 0 0 2 FP chr20 64096558 64097264 0 0 0 2 False 0 0 0 2 FP -chr20 64125009 64128074 3 3 2 0 True 12 12 0 0 TP -chr20 64131704 64134055 5 5 8 1 True 24 24 0 0 TP +chr20 64125009 64128074 3 3 2 0 True 2 2 0 0 TP +chr20 64131704 64134055 5 5 8 1 True 8 8 0 0 TP chr20 64134783 64136486 3 3 1 0 True 4 4 0 0 TP chr20 64157794 64159076 2 2 0 0 False 2 2 0 0 TP -chr20 64173309 64176629 4 4 7 3 True 17 17 0 0 TP +chr20 64173309 64176629 4 4 7 3 True 7 7 0 0 TP chr20 64201754 64202198 3 3 0 0 False 3 3 0 0 TP chr20 64232948 64233645 2 2 0 0 False 2 2 0 0 TP diff --git a/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json index 45426a73..eb604556 100644 --- a/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json +++ b/repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json @@ -1,11 +1,11 @@ { - "TP-base": 596, - "TP-comp": 596, - "FP": 16, + "TP-base": 555, + "TP-comp": 555, + "FP": 20, "FN": 2, - "precision": 0.9738562091503268, - "recall": 0.9966555183946488, - "f1": 0.9851239669421488, - "base cnt": 598, - "comp cnt": 612 + "precision": 0.9652173913043478, + "recall": 0.9964093357271095, + "f1": 0.980565371024735, + "base cnt": 557, + "comp cnt": 575 } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_three/log.txt b/repo_utils/answer_key/refine/refine_output_three/log.txt index fed78c17..c497a66d 100644 --- a/repo_utils/answer_key/refine/refine_output_three/log.txt +++ b/repo_utils/answer_key/refine/refine_output_three/log.txt @@ -1,6 +1,6 @@ -2025-02-03 00:52:06,929 [INFO] Truvari v5.1.0 -2025-02-03 00:52:06,930 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -f repo_utils/test_files/refine_data/chr20.fa.gz -s 5 -o test_results/refine_output_three --refine -2025-02-03 00:52:06,930 [INFO] Params: +2025-02-16 01:48:46,734 [INFO] Truvari v5.1.1 +2025-02-16 01:48:46,735 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -f repo_utils/test_files/refine_data/chr20.fa.gz -s 5 -o test_results/refine_output_three --refine +2025-02-16 01:48:46,736 [INFO] Params: { "base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", @@ -36,10 +36,10 @@ "skip_gt": false, "max_resolve": 25000 } -2025-02-03 00:52:06,974 [INFO] Including 225 bed regions -2025-02-03 00:52:10,396 [INFO] Zipped 7157 variants Counter({'comp': 5302, 'base': 1855}) -2025-02-03 00:52:10,397 [INFO] 211 chunks of 7157 variants Counter({'__filtered': 6137, 'base': 569, 'comp': 451}) -2025-02-03 00:52:10,500 [INFO] Stats: { +2025-02-16 01:48:46,783 [INFO] Including 225 bed regions +2025-02-16 01:48:50,423 [INFO] Zipped 7157 variants Counter({'comp': 5302, 'base': 1855}) +2025-02-16 01:48:50,424 [INFO] 211 chunks of 7157 variants Counter({'__filtered': 6137, 'base': 569, 'comp': 451}) +2025-02-16 01:48:50,541 [INFO] Stats: { "TP-base": 387, "TP-comp": 387, "FP": 64, @@ -71,13 +71,13 @@ } } } -2025-02-03 00:52:10,500 [INFO] Finished bench -2025-02-03 00:52:10,509 [INFO] Truvari v5.1.0 -2025-02-03 00:52:10,511 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -f repo_utils/test_files/refine_data/chr20.fa.gz -s 5 -o test_results/refine_output_three --refine -2025-02-03 00:52:10,512 [INFO] Params: +2025-02-16 01:48:50,542 [INFO] Finished bench +2025-02-16 01:48:50,551 [INFO] Truvari v5.1.1 +2025-02-16 01:48:50,552 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -f repo_utils/test_files/refine_data/chr20.fa.gz -s 5 -o test_results/refine_output_three --refine +2025-02-16 01:48:50,553 [INFO] Params: { "benchdir": "test_results/refine_output_three", - "align": "mafft", + "align": "poa", "use_original_vcfs": false, "write_phab": false, "threads": 4, @@ -89,29 +89,29 @@ "mafft_params": "--auto --thread 1", "debug": false } -2025-02-03 00:52:10,513 [INFO] Setting up regions -2025-02-03 00:52:10,546 [INFO] 82 --regions reduced to 82 after intersecting with 225 from --includebed -2025-02-03 00:52:10,547 [INFO] Extending the regions by 100 bases -2025-02-03 00:52:10,885 [INFO] 72 regions to be refined -2025-02-03 00:52:10,891 [WARNING] Harmonizing variants ≥50kbp is not recommended -2025-02-03 00:52:10,892 [INFO] Preparing regions -2025-02-03 00:52:10,899 [INFO] Extracting haplotypes -2025-02-03 00:52:11,228 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:888: CoverageWarning:No data was collected. (no-data-collected) -2025-02-03 00:52:11,231 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:888: CoverageWarning:No data was collected. (no-data-collected) -2025-02-03 00:52:11,240 [INFO] Harmonizing variants -2025-02-03 00:52:26,723 [INFO] Running bench -2025-02-03 00:52:26,746 [INFO] Including 72 bed regions -2025-02-03 00:52:28,444 [INFO] Zipped 5070 variants Counter({'base': 2535, 'comp': 2535}) -2025-02-03 00:52:28,445 [INFO] 71 chunks of 5070 variants Counter({'__filtered': 4520, 'base': 290, 'comp': 260}) -2025-02-03 00:52:29,625 [INFO] Stats: { - "TP-base": 465, - "TP-comp": 411, - "FP": 40, - "FN": 104, - "precision": 0.9113082039911308, - "recall": 0.8172231985940246, - "f1": 0.861705149535365, +2025-02-16 01:48:50,553 [INFO] Setting up regions +2025-02-16 01:48:50,587 [INFO] 82 --regions reduced to 82 after intersecting with 225 from --includebed +2025-02-16 01:48:50,588 [INFO] Extending the regions by 100 bases +2025-02-16 01:48:50,947 [INFO] 72 regions to be refined +2025-02-16 01:48:50,953 [WARNING] Harmonizing variants ≥50kbp is not recommended +2025-02-16 01:48:50,954 [INFO] Preparing regions +2025-02-16 01:48:50,962 [INFO] Extracting haplotypes +2025-02-16 01:48:51,342 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:892: CoverageWarning:No data was collected. (no-data-collected) +2025-02-16 01:48:51,345 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:892: CoverageWarning:No data was collected. (no-data-collected) +2025-02-16 01:48:51,358 [INFO] Harmonizing variants +2025-02-16 01:48:52,687 [INFO] Running bench +2025-02-16 01:48:52,727 [INFO] Including 72 bed regions +2025-02-16 01:48:54,465 [INFO] Zipped 4340 variants Counter({'base': 2170, 'comp': 2170}) +2025-02-16 01:48:54,466 [INFO] 74 chunks of 4340 variants Counter({'__filtered': 3806, 'base': 282, 'comp': 252}) +2025-02-16 01:48:55,604 [INFO] Stats: { + "TP-base": 477, + "TP-comp": 414, + "FP": 37, + "FN": 92, + "precision": 0.917960088691796, + "recall": 0.8383128295254832, + "f1": 0.876330451105298, "base cnt": 569, "comp cnt": 451 } -2025-02-03 00:52:29,625 [INFO] Finished refine +2025-02-16 01:48:55,605 [INFO] Finished refine diff --git a/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz index e5d31039..5bab0291 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz.tbi index 92123cac..6b2df02a 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab.output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/candidate.refine.bed b/repo_utils/answer_key/refine/refine_output_three/phab_bench/candidate.refine.bed index 75b691b7..5b2aae2f 100644 --- a/repo_utils/answer_key/refine/refine_output_three/phab_bench/candidate.refine.bed +++ b/repo_utils/answer_key/refine/refine_output_three/phab_bench/candidate.refine.bed @@ -1,30 +1,31 @@ -chr20 2240950 2241281 -chr20 4032347 4033346 -chr20 14861956 14862620 +chr20 641935 642272 +chr20 2240968 2241243 +chr20 4032691 4033209 +chr20 5041953 5042278 +chr20 10802717 10802854 chr20 16257844 16259215 -chr20 18209129 18210249 -chr20 20354902 20357861 -chr20 21721596 21721710 -chr20 22082256 22083544 +chr20 18209129 18210025 +chr20 20337319 20337634 +chr20 20355047 20355445 +chr20 20356529 20357803 +chr20 22082256 22083442 chr20 23155541 23155867 -chr20 35580680 35580870 -chr20 38123851 38124122 -chr20 50775888 50775909 +chr20 35580676 35580766 +chr20 38123851 38124009 +chr20 38463987 38464354 +chr20 48449784 48450395 chr20 55624798 55625662 chr20 55627628 55628315 -chr20 55944262 55945295 -chr20 56280531 56281724 -chr20 57090858 57091284 -chr20 57350847 57350930 -chr20 57948991 57949450 -chr20 59384469 59384694 -chr20 60314410 60314737 -chr20 61282821 61283489 -chr20 62321386 62321740 -chr20 62349631 62349904 -chr20 62360425 62360692 +chr20 56280518 56281823 +chr20 57090858 57091172 +chr20 57949040 57949343 +chr20 60314410 60314721 +chr20 62270590 62270837 +chr20 62321386 62321565 +chr20 62349631 62349830 +chr20 62360425 62360596 +chr20 62875249 62875294 chr20 63154677 63154931 -chr20 63693446 63693676 -chr20 63948617 63948750 -chr20 64131937 64133833 -chr20 64173531 64176450 \ No newline at end of file +chr20 63491947 63492217 +chr20 63559420 63559729 +chr20 64126743 64127885 \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz index ea360288..d18e3d8c 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz.tbi index 6e02d777..2b18b281 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz index 5233f79d..1c6760e6 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz.tbi index f25473e3..351ec0e6 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/params.json b/repo_utils/answer_key/refine/refine_output_three/phab_bench/params.json index 49c25875..ed1024d9 100644 --- a/repo_utils/answer_key/refine/refine_output_three/phab_bench/params.json +++ b/repo_utils/answer_key/refine/refine_output_three/phab_bench/params.json @@ -1 +1 @@ -{"base": "test_results/refine_output_three/phab.output.vcf.gz", "comp": "test_results/refine_output_three/phab.output.vcf.gz", "output": "test_results/refine_output_three/phab_bench", "includebed": "/tmp/yehkrzlt.bed", "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/refine_data/chr20.fa.gz", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "bnddist": 100, "sizemin": 5, "sizefilt": 5, "sizemax": -1, "passonly": false, "no_ref": "a", "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": true, "short_circuit": true, "skip_gt": false, "max_resolve": 25000} \ No newline at end of file +{"base": "test_results/refine_output_three/phab.output.vcf.gz", "comp": "test_results/refine_output_three/phab.output.vcf.gz", "output": "test_results/refine_output_three/phab_bench", "includebed": "/tmp/7s1spfvy.bed", "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/refine_data/chr20.fa.gz", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "bnddist": 100, "sizemin": 5, "sizefilt": 5, "sizemax": -1, "passonly": false, "no_ref": "a", "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": true, "short_circuit": true, "skip_gt": false, "max_resolve": 25000} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json b/repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json index 377143c9..571d99fd 100644 --- a/repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json +++ b/repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json @@ -1,31 +1,30 @@ { - "TP-base": 227, - "TP-comp": 227, - "FP": 33, - "FN": 63, - "precision": 0.8730769230769231, - "recall": 0.7827586206896552, - "f1": 0.8254545454545456, - "base cnt": 290, - "comp cnt": 260, - "TP-comp_TP-gt": 216, - "TP-comp_FP-gt": 11, - "TP-base_TP-gt": 216, - "TP-base_FP-gt": 11, - "gt_concordance": 0.9515418502202643, + "TP-base": 237, + "TP-comp": 237, + "FP": 15, + "FN": 45, + "precision": 0.9404761904761905, + "recall": 0.8404255319148937, + "f1": 0.8876404494382023, + "base cnt": 282, + "comp cnt": 252, + "TP-comp_TP-gt": 221, + "TP-comp_FP-gt": 16, + "TP-base_TP-gt": 221, + "TP-base_FP-gt": 16, + "gt_concordance": 0.9324894514767933, "gt_matrix": { - "(1, 0)": { - "(0, 1)": 105 - }, "(0, 1)": { - "(1, 0)": 86, - "(1, 1)": 2, - "(0, 1)": 4 + "(1, 0)": 85, + "(1, 1)": 2 + }, + "(1, 0)": { + "(0, 1)": 123 }, "(1, 1)": { - "(0, 1)": 7, - "(1, 1)": 21, - "(1, 0)": 2 + "(1, 0)": 4, + "(1, 1)": 13, + "(0, 1)": 10 } } } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz index 739a237e..149fb683 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz.tbi index fb94c36a..db7ee3b7 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz index c020e12a..b6fef394 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz.tbi index 09d57497..dd8bb7fb 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/phab_bench/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.base.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/refine.base.vcf.gz index 03fccf52..64502a90 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/refine.base.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/refine.base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/refine.base.vcf.gz.tbi index a9bb8f7e..fb9bb613 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/refine.base.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/refine.base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_three/refine.comp.vcf.gz index f08b3c1a..0c3640bb 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/refine.comp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_three/refine.comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_three/refine.comp.vcf.gz.tbi index a55580c5..f296c8fd 100644 Binary files a/repo_utils/answer_key/refine/refine_output_three/refine.comp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_three/refine.comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json index 2a3d56be..12418ad5 100644 --- a/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json +++ b/repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json @@ -1,18 +1,18 @@ { - "TP": 40, - "TN": 1, - "FP": 27, - "FN": 28, - "base P": 72, - "base N": 10, - "comp P": 80, - "comp N": 2, - "PPV": 0.5, - "TPR": 0.5555555555555556, - "TNR": 0.1, - "NPV": 0.5, + "TP": 41, + "TN": 0, + "FP": 19, + "FN": 26, + "base P": 73, + "base N": 9, + "comp P": 81, + "comp N": 1, + "PPV": 0.5061728395061729, + "TPR": 0.5616438356164384, + "TNR": 0.0, + "NPV": 0.0, "ACC": 0.5, - "BA": 0.3277777777777778, - "F1": 0.5263157894736842, + "BA": 0.2808219178082192, + "F1": 0.5324675324675325, "UND": 0 } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt index 94a48cb9..c2bcb0d3 100644 --- a/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt +++ b/repo_utils/answer_key/refine/refine_output_three/refine.regions.txt @@ -1,83 +1,83 @@ chrom start end in_tpbase in_tp in_fn in_fp refined out_tpbase out_tp out_fn out_fp state -chr20 278819 279179 3 3 1 0 True 5 5 0 0 TP -chr20 641802 642530 3 3 2 0 True 4 4 0 0 TP -chr20 2240850 2241400 1 1 4 1 True 1 1 4 1 FN,FP -chr20 4032247 4033338 2 2 2 1 True 2 2 2 2 FN,FP +chr20 278819 279179 3 3 1 0 True 3 3 0 0 TP +chr20 641802 642530 3 3 2 0 True 4 4 1 0 FN +chr20 2240850 2241400 1 1 4 1 True 2 2 2 0 FN +chr20 4032247 4033338 2 2 2 1 True 2 2 0 1 FP chr20 5040366 5040587 0 0 0 2 False 0 0 0 2 FP -chr20 5041831 5042378 1 1 1 1 True 2 2 0 0 TP +chr20 5041831 5042378 1 1 1 1 True 2 2 0 3 FP chr20 8661834 8662229 1 1 3 1 True 4 4 0 0 TP -chr20 10802617 10802954 1 1 1 0 True 1 1 0 0 TP +chr20 10802617 10802954 1 1 1 0 True 2 2 0 2 FP chr20 13848162 13848654 3 3 1 0 True 3 3 0 0 TP -chr20 14861944 14862754 5 5 5 1 True 6 6 1 0 FN -chr20 16257744 16259315 2 2 2 0 True 2 2 2 0 FN -chr20 16395091 16395483 3 3 1 0 True 3 3 0 0 TP -chr20 18209029 18210244 3 3 2 1 True 6 6 0 2 FP +chr20 14861944 14862754 5 5 5 1 True 11 11 0 0 TP +chr20 16257744 16259315 2 2 2 0 True 2 2 3 0 FN +chr20 16395091 16395483 3 3 1 0 True 4 4 0 0 TP +chr20 18209029 18210244 3 3 2 1 True 3 3 0 1 FP chr20 20295904 20296440 2 2 2 1 True 5 5 0 0 TP -chr20 20320229 20320629 1 1 2 1 True 4 4 0 0 TP -chr20 20337175 20337734 1 1 6 2 True 3 3 0 0 TP -chr20 20354802 20355545 3 3 1 0 True 4 4 1 0 FN -chr20 20356420 20357920 4 4 7 1 True 9 9 2 0 FN -chr20 21721341 21721756 2 2 1 0 True 3 3 0 1 FP -chr20 22082156 22084015 4 4 3 1 True 3 3 4 1 FN,FP +chr20 20320229 20320629 1 1 2 1 True 2 2 0 0 TP +chr20 20337175 20337734 1 1 6 2 True 4 4 1 0 FN +chr20 20354802 20355545 3 3 1 0 True 5 5 2 1 FN,FP +chr20 20356420 20357920 4 4 7 1 True 9 9 1 0 FN +chr20 21721341 21721756 2 2 1 0 True 2 2 0 0 TP +chr20 22082156 22084015 4 4 3 1 True 4 4 3 0 FN chr20 23155468 23155967 3 3 2 2 True 4 4 1 1 FN,FP chr20 23560829 23561208 1 1 2 2 True 2 2 0 0 TP -chr20 24681956 24682235 2 2 1 0 True 1 1 0 0 TP +chr20 24681956 24682235 2 2 1 0 True 2 2 0 0 TP chr20 25781680 25781901 0 0 0 1 False 0 0 0 1 FP chr20 32722934 32723155 0 0 1 0 False 0 0 1 0 FN -chr20 34235788 34236091 0 0 2 1 True 2 2 0 0 TP -chr20 35580576 35580866 1 1 2 1 True 3 3 2 1 FN,FP -chr20 38123689 38124113 2 2 1 4 True 3 3 3 4 FN,FP -chr20 38463887 38464454 2 2 2 0 True 3 3 0 0 TP -chr20 41196260 41196605 3 3 1 0 True 4 4 0 0 TP +chr20 34235788 34236091 0 0 2 1 True 1 1 0 0 TP +chr20 35580576 35580866 1 1 2 1 True 1 1 2 1 FN,FP +chr20 38123689 38124113 2 2 1 4 True 5 5 0 3 FP +chr20 38463887 38464454 2 2 2 0 True 3 3 1 0 FN +chr20 41196260 41196605 3 3 1 0 True 3 3 0 0 TP chr20 41257604 41258113 0 0 0 1 False 0 0 0 1 FP -chr20 44764040 44764313 2 2 1 0 True 1 1 0 0 TP -chr20 45600545 45600805 2 2 2 0 True 2 2 0 0 TP -chr20 48449684 48450495 4 4 2 0 True 5 5 0 0 TP +chr20 44764040 44764313 2 2 1 0 True 3 3 0 0 TP +chr20 45600545 45600805 2 2 2 0 True 3 3 0 0 TP +chr20 48449684 48450495 4 4 2 0 True 5 5 1 0 FN chr20 49834072 49834579 2 2 1 0 True 2 2 0 0 TP -chr20 50775536 50775942 1 1 2 1 True 1 1 0 1 FP +chr20 50775536 50775942 1 1 2 1 True 2 2 0 0 TP chr20 51953709 51953930 0 0 0 1 False 0 0 0 1 FP chr20 53203989 53204362 2 2 2 1 True 2 2 0 0 TP -chr20 55624698 55625762 6 6 6 0 True 7 7 9 1 FN,FP -chr20 55627528 55628415 7 7 3 0 True 7 7 1 2 FN,FP -chr20 55944162 55945285 2 2 2 1 True 2 2 2 0 FN -chr20 56280431 56282023 4 4 5 1 True 4 4 2 1 FN,FP -chr20 57090758 57091276 1 1 2 0 True 2 2 1 0 FN +chr20 55624698 55625762 6 6 6 0 True 10 10 6 1 FN,FP +chr20 55627528 55628415 7 7 3 0 True 7 7 2 0 FN +chr20 55944162 55945285 2 2 2 1 True 3 3 0 0 TP +chr20 56280431 56282023 4 4 5 1 True 14 14 3 0 FN +chr20 57090758 57091276 1 1 2 0 True 1 1 2 0 FN chr20 57190146 57190538 0 0 3 1 True 1 1 0 0 TP -chr20 57350746 57351030 1 1 1 0 True 1 1 1 0 FN -chr20 57948891 57949456 1 1 4 1 True 1 1 4 1 FN,FP -chr20 59384256 59384853 3 3 2 0 True 4 4 1 0 FN -chr20 60314333 60314821 2 2 2 0 True 2 2 1 0 FN -chr20 60702895 60703197 2 2 2 1 True 3 3 0 0 TP -chr20 61100811 61102515 1 1 4 1 True 4 4 0 0 TP -chr20 61201712 61202352 2 2 4 1 True 3 3 0 0 TP -chr20 61282815 61283589 4 4 2 0 True 5 5 1 0 FN +chr20 57350746 57351030 1 1 1 0 True 2 2 0 0 TP +chr20 57948891 57949456 1 1 4 1 True 2 2 1 0 FN +chr20 59384256 59384853 3 3 2 0 True 5 5 0 0 TP +chr20 60314333 60314821 2 2 2 0 True 2 2 2 0 FN +chr20 60702895 60703197 2 2 2 1 True 2 2 0 0 TP +chr20 61100811 61102515 1 1 4 1 True 2 2 0 0 TP +chr20 61201712 61202352 2 2 4 1 True 2 2 0 0 TP +chr20 61282815 61283589 4 4 2 0 True 4 4 0 0 TP chr20 61289552 61290383 1 1 1 1 True 2 2 0 0 TP chr20 61329235 61329551 0 0 0 2 False 0 0 0 2 FP chr20 61561999 61562362 0 0 2 1 True 1 1 0 0 TP chr20 62057492 62058878 1 1 3 1 True 2 2 0 0 TP -chr20 62270303 62270937 1 1 3 1 True 4 4 0 0 TP -chr20 62321286 62321840 2 2 3 0 True 2 2 3 0 FN -chr20 62349531 62349936 1 1 5 1 True 1 1 2 1 FN,FP -chr20 62360300 62360712 0 0 7 2 True 4 4 2 1 FN,FP -chr20 62830540 62830807 2 2 1 1 True 1 1 0 0 TP -chr20 62875131 62875514 2 2 3 0 True 2 2 0 0 TP -chr20 63027956 63029140 4 4 1 1 True 3 3 0 0 TP -chr20 63048983 63049269 3 3 1 0 True 2 2 0 0 TP +chr20 62270303 62270937 1 1 3 1 True 3 3 1 0 FN +chr20 62321286 62321840 2 2 3 0 True 2 2 2 0 FN +chr20 62349531 62349936 1 1 5 1 True 4 4 1 0 FN +chr20 62360300 62360712 0 0 7 2 True 5 5 2 0 FN +chr20 62830540 62830807 2 2 1 1 True 3 3 0 0 TP +chr20 62875131 62875514 2 2 3 0 True 2 2 1 0 FN +chr20 63027956 63029140 4 4 1 1 True 4 4 0 0 TP +chr20 63048983 63049269 3 3 1 0 True 4 4 0 0 TP chr20 63154577 63155031 1 1 1 0 True 1 1 1 0 FN chr20 63167363 63167674 2 2 1 0 True 3 3 0 0 TP chr20 63221399 63221831 1 1 2 1 True 2 2 0 0 TP -chr20 63491847 63492500 1 1 3 1 True 4 4 0 0 TP -chr20 63535641 63536112 1 1 2 0 True 0 0 0 0 TN -chr20 63559305 63559829 1 1 2 1 True 5 5 0 0 TP -chr20 63641737 63642125 1 1 2 1 True 3 3 0 0 TP -chr20 63693339 63693842 1 1 6 1 True 10 10 1 0 FN +chr20 63491847 63492500 1 1 3 1 True 2 2 2 0 FN +chr20 63535641 63536112 1 1 2 0 True 1 1 0 0 TP +chr20 63559305 63559829 1 1 2 1 True 3 3 1 0 FN +chr20 63641737 63642125 1 1 2 1 True 2 2 0 0 TP +chr20 63693339 63693842 1 1 6 1 True 2 2 0 0 TP chr20 63770826 63771124 0 0 0 2 False 0 0 0 2 FP -chr20 63948484 63948763 2 2 1 1 True 2 2 0 1 FP -chr20 63964695 63966223 1 1 1 0 True 2 2 0 0 TP +chr20 63948484 63948763 2 2 1 1 True 2 2 0 0 TP +chr20 63964695 63966223 1 1 1 0 True 1 1 0 0 TP chr20 64065772 64065993 0 0 0 1 False 0 0 0 1 FP chr20 64090623 64091117 0 0 0 2 False 0 0 0 2 FP chr20 64096929 64097150 0 0 0 2 False 0 0 0 2 FP -chr20 64125250 64127985 3 3 2 0 True 3 3 0 0 TP -chr20 64131803 64133966 5 5 8 1 True 5 5 6 5 FN,FP -chr20 64134880 64136440 3 3 1 0 True 3 3 0 0 TP -chr20 64173328 64176440 4 4 7 3 True 9 9 3 6 FN,FP +chr20 64125250 64127985 3 3 2 0 True 2 2 0 1 FP +chr20 64131803 64133966 5 5 8 1 True 5 5 0 0 TP +chr20 64134880 64136440 3 3 1 0 True 4 4 0 0 TP +chr20 64173328 64176440 4 4 7 3 True 7 7 0 0 TP diff --git a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json index 6918636d..841b508c 100644 --- a/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json +++ b/repo_utils/answer_key/refine/refine_output_three/refine.variant_summary.json @@ -1,11 +1,11 @@ { - "TP-base": 465, - "TP-comp": 411, - "FP": 40, - "FN": 104, - "precision": 0.9113082039911308, - "recall": 0.8172231985940246, - "f1": 0.861705149535365, + "TP-base": 477, + "TP-comp": 414, + "FP": 37, + "FN": 92, + "precision": 0.917960088691796, + "recall": 0.8383128295254832, + "f1": 0.876330451105298, "base cnt": 569, "comp cnt": 451 } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/log.txt b/repo_utils/answer_key/refine/refine_output_two/log.txt index d2f8a682..bf4e81ab 100644 --- a/repo_utils/answer_key/refine/refine_output_two/log.txt +++ b/repo_utils/answer_key/refine/refine_output_two/log.txt @@ -1,6 +1,6 @@ -2025-02-02 20:26:13,929 [INFO] Truvari v5.0.1.dev0+895b8e1.uc -2025-02-02 20:26:13,930 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_two -2025-02-02 20:26:13,931 [INFO] Params: +2025-02-16 01:48:34,959 [INFO] Truvari v5.1.1 +2025-02-16 01:48:34,960 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/refine_data/hg002_base.vcf.gz -c repo_utils/test_files/refine_data/hg002_comp.vcf.gz --includebed repo_utils/test_files/refine_data/h1_hc_tr_hg002.bed -s 5 -o test_results/refine_output_two +2025-02-16 01:48:34,961 [INFO] Params: { "base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", @@ -36,10 +36,10 @@ "skip_gt": false, "max_resolve": 25000 } -2025-02-02 20:26:13,974 [INFO] Including 225 bed regions -2025-02-02 20:26:17,240 [INFO] Zipped 7157 variants Counter({'comp': 5302, 'base': 1855}) -2025-02-02 20:26:17,241 [INFO] 211 chunks of 7157 variants Counter({'__filtered': 6137, 'base': 569, 'comp': 451}) -2025-02-02 20:26:17,341 [INFO] Stats: { +2025-02-16 01:48:35,009 [INFO] Including 225 bed regions +2025-02-16 01:48:38,565 [INFO] Zipped 7157 variants Counter({'comp': 5302, 'base': 1855}) +2025-02-16 01:48:38,566 [INFO] 211 chunks of 7157 variants Counter({'__filtered': 6137, 'base': 569, 'comp': 451}) +2025-02-16 01:48:38,680 [INFO] Stats: { "TP-base": 387, "TP-comp": 387, "FP": 64, @@ -71,4 +71,4 @@ } } } -2025-02-02 20:26:17,342 [INFO] Finished bench +2025-02-16 01:48:38,681 [INFO] Finished bench diff --git a/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz index 775d8cc5..247724c4 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz and b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi index da6e5ff8..75a0cd74 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_two/phab.output.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json b/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json index 4199584e..f888a302 100644 --- a/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json +++ b/repo_utils/answer_key/refine/refine_output_two/phab_bench/params.json @@ -1 +1 @@ -{"base": "test_results/refine_output_two/phab.output.vcf.gz", "comp": "test_results/refine_output_two/phab.output.vcf.gz", "output": "test_results/refine_output_two/phab_bench", "includebed": "/tmp/wudtjel_.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "bnddist": 100, "sizemin": 5, "sizefilt": 5, "sizemax": -1, "passonly": false, "no_ref": "a", "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": true, "short_circuit": true, "skip_gt": false, "max_resolve": 25000} \ No newline at end of file +{"base": "test_results/refine_output_two/phab.output.vcf.gz", "comp": "test_results/refine_output_two/phab.output.vcf.gz", "output": "test_results/refine_output_two/phab_bench", "includebed": "/tmp/mwbh6toq.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "bnddist": 100, "sizemin": 5, "sizefilt": 5, "sizemax": -1, "passonly": false, "no_ref": "a", "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": true, "short_circuit": true, "skip_gt": false, "max_resolve": 25000} \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json b/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json index 8ce870dd..e38ed21c 100644 --- a/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json +++ b/repo_utils/answer_key/refine/refine_output_two/phab_bench/summary.json @@ -1,27 +1,27 @@ { - "TP-base": 247, - "TP-comp": 247, + "TP-base": 206, + "TP-comp": 206, "FP": 2, "FN": 1, - "precision": 0.9919678714859438, - "recall": 0.9959677419354839, - "f1": 0.993963782696177, - "base cnt": 248, - "comp cnt": 249, - "TP-comp_TP-gt": 247, + "precision": 0.9903846153846154, + "recall": 0.9951690821256038, + "f1": 0.9927710843373494, + "base cnt": 207, + "comp cnt": 208, + "TP-comp_TP-gt": 206, "TP-comp_FP-gt": 0, - "TP-base_TP-gt": 247, + "TP-base_TP-gt": 206, "TP-base_FP-gt": 0, "gt_concordance": 1.0, "gt_matrix": { "(0, 1)": { - "(1, 0)": 102 + "(1, 0)": 84 }, "(1, 0)": { - "(0, 1)": 107 + "(0, 1)": 98 }, "(1, 1)": { - "(1, 1)": 38 + "(1, 1)": 24 } } } \ No newline at end of file diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz index d090cbeb..48d77213 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi index 2e8233ed..4958d755 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz index cf5af7da..f7ae26b1 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi index 2e8233ed..eec80079 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_two/phab_bench/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.base.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/refine.base.vcf.gz index 0cb619c8..c4e87587 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/refine.base.vcf.gz and b/repo_utils/answer_key/refine/refine_output_two/refine.base.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.base.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/refine.base.vcf.gz.tbi index ccb0f211..486b343d 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/refine.base.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_two/refine.base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.comp.vcf.gz b/repo_utils/answer_key/refine/refine_output_two/refine.comp.vcf.gz index e81dc633..57d506f6 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/refine.comp.vcf.gz and b/repo_utils/answer_key/refine/refine_output_two/refine.comp.vcf.gz differ diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.comp.vcf.gz.tbi b/repo_utils/answer_key/refine/refine_output_two/refine.comp.vcf.gz.tbi index 90dace43..54f97f9b 100644 Binary files a/repo_utils/answer_key/refine/refine_output_two/refine.comp.vcf.gz.tbi and b/repo_utils/answer_key/refine/refine_output_two/refine.comp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.log.txt b/repo_utils/answer_key/refine/refine_output_two/refine.log.txt index 6453b16e..31b3bef4 100644 --- a/repo_utils/answer_key/refine/refine_output_two/refine.log.txt +++ b/repo_utils/answer_key/refine/refine_output_two/refine.log.txt @@ -1,89 +1,43 @@ -2025-02-02 20:26:18,864 [INFO] Truvari v5.0.1.dev0+895b8e1.uc -2025-02-02 20:26:18,865 [INFO] Command /data/truvari/__main__.py refine --buffer 101 --write-phab --use-original-vcfs --subset --regions repo_utils/test_files/refine_data/h2_hc_tr_hg002.bed -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_two -2025-02-02 20:26:18,866 [INFO] Params: +2025-02-16 01:48:40,286 [INFO] Truvari v5.1.1 +2025-02-16 01:48:40,299 [INFO] Command /data/truvari/__main__.py refine --buffer 101 --write-phab --use-original-vcfs --subset --regions repo_utils/test_files/refine_data/h2_hc_tr_hg002.bed -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_two +2025-02-16 01:48:40,300 [INFO] Params: { "benchdir": "test_results/refine_output_two", - "align": "mafft", + "align": "poa", "use_original_vcfs": true, "write_phab": true, "threads": 4, "buffer": 101, "reference": "repo_utils/test_files/refine_data/chr20.fa.gz", "regions": "repo_utils/test_files/refine_data/h2_hc_tr_hg002.bed", - "coords": "reg", + "coords": "R", "subset": true, "mafft_params": "--auto --thread 1", "debug": false } -2025-02-02 20:26:18,867 [INFO] Setting up regions -2025-02-02 20:26:18,916 [INFO] 225 --includebed reduced to 129 after intersecting with 247 from --regions -2025-02-02 20:26:18,917 [INFO] Extending the regions by 101 bases -2025-02-02 20:26:19,632 [INFO] 46 regions to be refined -2025-02-02 20:26:19,642 [WARNING] Harmonizing variants ≥50kbp is not recommended -2025-02-02 20:26:19,643 [INFO] Preparing regions -2025-02-02 20:26:19,648 [INFO] Extracting haplotypes -2025-02-02 20:26:19,854 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,864 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,882 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,891 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,898 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,906 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,921 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,930 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,942 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,956 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:19,997 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,025 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,035 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,039 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,041 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,045 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,055 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,063 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,067 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,070 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,075 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,082 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,093 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,104 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,114 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,126 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,135 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,140 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,146 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,155 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,160 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,164 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,167 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,170 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,173 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,177 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,181 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,186 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,195 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,200 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,206 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,214 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,223 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,245 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,258 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,286 [WARNING] Harmonizing unphased variants may have undesired behavior!! -2025-02-02 20:26:20,344 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:888: CoverageWarning:No data was collected. (no-data-collected) -2025-02-02 20:26:20,347 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:888: CoverageWarning:No data was collected. (no-data-collected) -2025-02-02 20:26:20,364 [INFO] Harmonizing variants -2025-02-02 20:26:21,549 [INFO] Running bench -2025-02-02 20:26:21,573 [INFO] Including 46 bed regions -2025-02-02 20:26:22,984 [INFO] Zipped 2608 variants Counter({'base': 1304, 'comp': 1304}) -2025-02-02 20:26:22,985 [INFO] 47 chunks of 2608 variants Counter({'__filtered': 2111, 'comp': 249, 'base': 248}) -2025-02-02 20:26:23,721 [INFO] Stats: { - "TP-base": 247, - "TP-comp": 247, +2025-02-16 01:48:40,322 [INFO] Setting up regions +2025-02-16 01:48:40,371 [INFO] 247 --regions reduced to 129 after intersecting with 225 from --includebed +2025-02-16 01:48:40,372 [INFO] Extending the regions by 101 bases +2025-02-16 01:48:41,160 [INFO] 46 regions to be refined +2025-02-16 01:48:41,171 [WARNING] Harmonizing variants ≥50kbp is not recommended +2025-02-16 01:48:41,172 [INFO] Preparing regions +2025-02-16 01:48:41,176 [INFO] Extracting haplotypes +2025-02-16 01:48:41,902 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:892: CoverageWarning:No data was collected. (no-data-collected) +2025-02-16 01:48:41,905 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:892: CoverageWarning:No data was collected. (no-data-collected) +2025-02-16 01:48:41,921 [INFO] Harmonizing variants +2025-02-16 01:48:43,237 [INFO] Running bench +2025-02-16 01:48:43,257 [INFO] Including 46 bed regions +2025-02-16 01:48:44,462 [INFO] Zipped 2400 variants Counter({'base': 1200, 'comp': 1200}) +2025-02-16 01:48:44,463 [INFO] 48 chunks of 2400 variants Counter({'__filtered': 1985, 'comp': 208, 'base': 207}) +2025-02-16 01:48:45,078 [INFO] Stats: { + "TP-base": 206, + "TP-comp": 206, "FP": 2, "FN": 1, - "precision": 0.9919678714859438, - "recall": 0.9959677419354839, - "f1": 0.993963782696177, - "base cnt": 248, - "comp cnt": 249 + "precision": 0.9903846153846154, + "recall": 0.9951690821256038, + "f1": 0.9927710843373494, + "base cnt": 207, + "comp cnt": 208 } -2025-02-02 20:26:23,722 [INFO] Finished refine +2025-02-16 01:48:45,079 [INFO] Finished refine diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt index d88e2a5e..d8c09f74 100644 --- a/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt +++ b/repo_utils/answer_key/refine/refine_output_two/refine.regions.txt @@ -1,30 +1,30 @@ chrom start end in_tpbase in_tp in_fn in_fp refined out_tpbase out_tp out_fn out_fp state -chr20 278799 279287 3 3 1 0 True 5 5 0 0 TP +chr20 278799 279287 3 3 1 0 True 4 4 0 0 TP chr20 420454 420871 2 2 0 0 False 2 2 0 0 TP -chr20 641735 642566 3 3 2 0 True 5 5 0 0 TP +chr20 641735 642566 3 3 2 0 True 3 3 0 0 TP chr20 709628 710076 2 2 0 0 False 2 2 0 0 TP chr20 1149706 1150321 2 2 0 0 False 2 2 0 0 TP chr20 1257832 1260629 2 2 0 0 False 2 2 0 0 TP chr20 1301498 1302768 2 2 0 0 False 2 2 0 0 TP chr20 2442865 2444044 2 2 0 0 False 2 2 0 0 TP -chr20 4032118 4033702 2 2 2 1 True 4 4 0 0 TP +chr20 4032118 4033702 2 2 2 1 True 2 2 0 0 TP chr20 4482484 4482835 2 2 0 0 False 2 2 0 0 TP chr20 4844637 4845007 2 2 0 0 False 2 2 0 0 TP chr20 5039848 5040600 0 0 0 2 True 0 0 0 2 FP chr20 7435114 7435850 2 2 0 0 False 2 2 0 0 TP -chr20 8661810 8662758 1 1 3 1 True 9 9 0 0 TP +chr20 8661810 8662758 1 1 3 1 True 5 5 0 0 TP chr20 10977696 10978078 2 2 0 0 False 2 2 0 0 TP chr20 13848063 13848750 3 3 1 0 True 3 3 0 0 TP -chr20 14861836 14862842 5 5 5 1 True 15 15 0 0 TP +chr20 14861836 14862842 5 5 5 1 True 12 12 0 0 TP chr20 16226853 16228588 3 3 0 0 False 3 3 0 0 TP -chr20 16395048 16395522 3 3 1 0 True 3 3 0 0 TP +chr20 16395048 16395522 3 3 1 0 True 4 4 0 0 TP chr20 17081115 17081511 2 2 0 0 False 2 2 0 0 TP chr20 17197022 17197342 2 2 0 0 False 2 2 0 0 TP chr20 18208996 18210828 3 3 2 1 True 5 5 0 0 TP chr20 18675549 18676016 2 2 0 0 False 2 2 0 0 TP chr20 19663265 19663627 2 2 0 0 False 2 2 0 0 TP -chr20 20337099 20337808 1 1 6 2 True 3 3 0 0 TP -chr20 20354469 20358424 7 7 8 1 True 14 14 0 0 TP +chr20 20337099 20337808 1 1 6 2 True 9 9 0 0 TP +chr20 20354469 20358424 7 7 8 1 True 12 12 0 0 TP chr20 20458539 20459038 2 2 0 0 False 2 2 0 0 TP chr20 21120111 21120640 2 2 0 0 False 2 2 0 0 TP chr20 21721073 21721836 2 2 1 0 True 3 3 0 0 TP @@ -45,15 +45,15 @@ chr20 32724826 32725100 0 0 0 0 False 0 0 0 0 TN chr20 34205518 34206061 1 1 0 0 False 1 1 0 0 TP chr20 34235649 34236314 0 0 2 1 True 2 2 0 0 TP chr20 36642041 36642323 1 1 0 0 False 1 1 0 0 TP -chr20 38123489 38124806 2 2 1 4 True 7 7 0 0 TP +chr20 38123489 38124806 2 2 1 4 True 4 4 0 0 TP chr20 38194432 38194767 2 2 0 0 False 2 2 0 0 TP -chr20 41196109 41196749 3 3 1 0 True 4 4 0 0 TP -chr20 44763795 44764386 2 2 1 0 True 2 2 0 0 TP -chr20 45600468 45600847 2 2 2 0 True 2 2 0 0 TP +chr20 41196109 41196749 3 3 1 0 True 5 5 0 0 TP +chr20 44763795 44764386 2 2 1 0 True 3 3 0 0 TP +chr20 45600468 45600847 2 2 2 0 True 4 4 0 0 TP chr20 46788706 46789631 2 2 0 0 False 2 2 0 0 TP chr20 47225423 47225746 2 2 0 0 False 2 2 0 0 TP chr20 48390797 48391332 2 2 0 0 False 2 2 0 0 TP -chr20 48449604 48450562 4 4 2 0 True 6 6 0 0 TP +chr20 48449604 48450562 4 4 2 0 True 5 5 0 0 TP chr20 48959258 48959753 2 2 0 0 False 2 2 0 0 TP chr20 50258349 50258652 2 2 0 0 False 2 2 0 0 TP chr20 50666047 50666994 2 2 0 0 False 2 2 0 0 TP @@ -61,8 +61,8 @@ chr20 50853538 50854029 2 2 0 0 False 2 2 0 0 TP chr20 51500491 51500981 2 2 0 0 False 2 2 0 0 TP chr20 53203886 53204574 2 2 2 1 True 4 4 0 0 TP chr20 53415541 53415961 2 2 0 0 False 2 2 0 0 TP -chr20 55627243 55628551 7 7 3 0 True 8 8 0 0 TP -chr20 55943818 55945908 2 2 2 1 True 5 5 0 0 TP +chr20 55627243 55628551 7 7 3 0 True 9 9 0 0 TP +chr20 55943818 55945908 2 2 2 1 True 4 4 0 0 TP chr20 56284157 56284508 2 2 0 0 False 2 2 0 0 TP chr20 56710454 56711294 2 2 0 0 False 2 2 0 0 TP chr20 57110111 57110886 2 2 0 0 False 2 2 0 0 TP @@ -73,11 +73,11 @@ chr20 58519801 58520473 2 2 0 0 False 2 2 0 0 TP chr20 58694761 58695512 2 2 0 0 False 2 2 0 0 TP chr20 59441935 59442374 2 2 0 0 False 2 2 0 0 TP chr20 60087290 60088066 2 2 0 0 False 2 2 0 0 TP -chr20 60314229 60315121 2 2 2 0 True 5 5 0 0 TP +chr20 60314229 60315121 2 2 2 0 True 7 7 0 0 TP chr20 60763930 60764735 2 2 0 0 False 2 2 0 0 TP chr20 61176624 61177075 2 2 0 0 False 2 2 0 0 TP -chr20 61201582 61202575 2 2 4 1 True 7 7 0 0 TP -chr20 61282405 61283770 4 4 2 0 True 6 6 0 0 TP +chr20 61201582 61202575 2 2 4 1 True 6 6 0 0 TP +chr20 61282405 61283770 4 4 2 0 True 4 4 0 0 TP chr20 61329157 61329678 0 0 0 2 False 0 0 0 2 FP chr20 61331427 61331854 2 2 0 0 False 2 2 0 0 TP chr20 61337104 61337691 2 2 0 0 False 2 2 0 0 TP @@ -85,26 +85,26 @@ chr20 61475305 61475827 2 2 0 0 False 2 2 0 0 TP chr20 61744087 61744755 2 2 0 0 False 2 2 0 0 TP chr20 61783302 61784940 3 3 0 0 False 3 3 0 0 TP chr20 61919575 61921475 2 2 0 0 False 2 2 0 0 TP -chr20 62057472 62059240 1 1 3 1 True 7 7 0 0 TP +chr20 62057472 62059240 1 1 3 1 True 3 3 0 0 TP chr20 62212743 62213975 4 4 0 0 False 4 4 0 0 TP -chr20 62270178 62271195 1 1 3 1 True 4 4 0 0 TP +chr20 62270178 62271195 1 1 3 1 True 3 3 0 0 TP chr20 62317736 62318560 2 2 0 0 False 2 2 0 0 TP -chr20 62349511 62350033 1 1 5 1 True 6 6 0 0 TP +chr20 62349511 62350033 1 1 5 1 True 9 9 0 0 TP chr20 62417323 62418163 3 3 0 0 False 3 3 0 0 TP chr20 62422343 62422892 2 2 0 0 False 2 2 0 0 TP chr20 62504178 62504715 2 2 0 0 False 2 2 0 0 TP -chr20 62830511 62830939 2 2 1 1 True 2 2 0 0 TP +chr20 62830511 62830939 2 2 1 1 True 3 3 0 0 TP chr20 62875071 62875657 2 2 3 0 True 3 3 0 0 TP chr20 62986209 62986906 2 2 0 0 False 2 2 0 0 TP -chr20 63027896 63028267 2 2 1 0 True 4 4 0 0 TP +chr20 63027896 63028267 2 2 1 0 True 3 3 0 0 TP chr20 63028775 63029503 2 2 0 1 True 2 2 0 0 TP -chr20 63048932 63049513 3 3 1 0 True 2 2 0 0 TP +chr20 63048932 63049513 3 3 1 0 True 3 3 0 0 TP chr20 63068308 63068900 2 2 0 0 False 2 2 0 0 TP chr20 63103148 63103593 1 1 0 0 False 1 1 0 0 TP chr20 63156666 63157426 2 2 0 0 False 2 2 0 0 TP chr20 63158082 63158827 2 2 0 0 False 2 2 0 0 TP -chr20 63167286 63167728 2 2 1 0 True 3 3 0 0 TP -chr20 63221379 63221977 1 1 2 1 True 2 2 0 0 TP +chr20 63167286 63167728 2 2 1 0 True 5 5 0 0 TP +chr20 63221379 63221977 1 1 2 1 True 4 4 0 0 TP chr20 63235228 63235551 2 2 0 0 False 2 2 0 0 TP chr20 63293978 63294367 2 2 0 0 False 2 2 0 0 TP chr20 63303554 63304959 2 2 0 0 False 2 2 0 0 TP @@ -117,14 +117,14 @@ chr20 63491488 63493165 1 1 3 1 True 4 4 0 0 TP chr20 63559187 63560064 1 1 2 1 True 4 4 0 0 TP chr20 63641678 63642236 1 1 2 1 True 2 2 0 0 TP chr20 63669478 63670597 2 2 0 0 False 2 2 0 0 TP -chr20 63693224 63693985 1 1 6 1 True 10 10 0 0 TP +chr20 63693224 63693985 1 1 6 1 True 9 9 0 0 TP chr20 63770811 63771204 0 0 0 2 False 0 0 0 2 FP chr20 63824530 63825245 2 2 0 0 False 2 2 0 0 TP -chr20 63948413 63948859 2 2 1 1 True 3 3 0 0 TP +chr20 63948413 63948859 2 2 1 1 True 2 2 0 0 TP chr20 64090603 64091490 0 0 0 2 False 0 0 0 2 FP chr20 64096557 64097265 0 0 0 2 False 0 0 0 2 FP -chr20 64125008 64128075 3 3 2 0 True 10 10 0 0 TP -chr20 64131703 64134056 5 5 8 1 True 24 24 0 0 TP +chr20 64125008 64128075 3 3 2 0 True 2 2 0 0 TP +chr20 64131703 64134056 5 5 8 1 True 8 8 0 0 TP chr20 64134782 64136487 3 3 1 0 True 4 4 0 0 TP -chr20 64173308 64176630 4 4 7 3 True 17 17 0 0 TP +chr20 64173308 64176630 4 4 7 3 True 7 7 0 0 TP chr20 64232947 64233646 2 2 0 0 False 2 2 0 0 TP diff --git a/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json b/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json index 82b0a1ea..58326a01 100644 --- a/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json +++ b/repo_utils/answer_key/refine/refine_output_two/refine.variant_summary.json @@ -1,11 +1,11 @@ { - "TP-base": 247, - "TP-comp": 247, + "TP-base": 206, + "TP-comp": 206, "FP": 2, "FN": 1, - "precision": 0.9919678714859438, - "recall": 0.9959677419354839, - "f1": 0.993963782696177, - "base cnt": 248, - "comp cnt": 249 + "precision": 0.9903846153846154, + "recall": 0.9951690821256038, + "f1": 0.9927710843373494, + "base cnt": 207, + "comp cnt": 208 } \ No newline at end of file diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_01fbdc703f5d26e8cc5c22fd0cd1c1d1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_01fbdc703f5d26e8cc5c22fd0cd1c1d1.msa deleted file mode 100644 index 9834356f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_01fbdc703f5d26e8cc5c22fd0cd1c1d1.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:60314229-60315121 -cacttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgca -cacctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctg -tcctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccat -ccatttgtccttccttccttccttccttccttc---cttccttccttccttccttccttc -cttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaac -catcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatc -catccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatc -catcctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatc -cactcttccatccatccatccacccaccctt----------------ccatccatccatc -ctcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatc -catcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatc -ctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatccatc -ctcccatcctcccatccatccatccatcctcccatccgtccatccatccttccatccac- ----------------cctcccatccatccatcctcccatccatctaccctcccatccatc -catcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatc -tatccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcc -tcccataatctatcttcccatccatttgtccttccttccttccttccttccttccttcct -tcgttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccaccca -accatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatcta -tccat--------------------ccatcctcccatccatcctcccatcctcccatcca -ttctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccct -cccatccatccatcctcccatccatccacccttccatccatccatccacccacccttcca -tccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcct -cccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatcca -tccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatcca -tccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctccca -tcctcccatccatccatccatccatccatccatcctcccatcctcccatcctcccatcca -tcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccca -tccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcca -tccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccg -tgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaa -aaatgaaaaaaagaatatattgatttcaggccagttacataga ->syndip_2_chr20:60314229-60315121 -cacttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgca -cacctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctg -tcgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccat -ccatttg--------------------tccttc---cttccttccttccttccttccttc -cttccacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaac -catcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatc -catccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatc -catcctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatc -cacccttccatccatccatccacccacccttccatccatccatcctcccatccatccatc -ctcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatc -catcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatc -ctcccatccatctaccctcccatccatccatcctcccatccaccctcccatccatccatc -catccatccaccctctcatccatccatcctcccatccgtccatccatccttccatccacc -ctcccatccatccatcctcccatccatccatcctcccatccatctaccctcccatccatc -catcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatc -tatccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcc -tcccataatctatcttcccatccatttgtccttccttccttccttccttccttcc----- ----ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccaccca -accatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatcta -tccatccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatcca -ttctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccct -cccatccatccatcctcccatccatccacccttccatccatccatccacccacccttcca -tccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcct -cccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatcca -tccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatcca -tccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctccca -tcctc----ccatccatccatccatccatccatcctcccatcctcccatcctcccatcca -tcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccca -tccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcca -tccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccg -tgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaa -aaatgaaaaaaagaatatattgatttcaggccagttacataga ->p:HG002_1_chr20:60314229-60315121 -cacttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgca -cacctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctg -tcgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccat -ccatttg--------------------tccttc---cttccttccttccttccttccttc -cttccacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaac -catcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatc -catccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatc -catcctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatc -cacccttccatccatccatccacccacccttccatccatccatcctcccatccatccatc -ctcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatc -catcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatc -ctcccatccatctaccctcccatccatccatcctcccatccaccctcccatccatccatc -catccatccaccctctcatccatccatcctcccatccgtccatccatccttccatccacc -ctcccatccatccatcctcccatccatccatcctcccatccatctaccctcccatccatc -catcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatc -tatccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcc -tcccataatctatcttcccatccatttgtccttccttccttccttccttccttcc----- ----ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccaccca -accatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatcta -tccatccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatcca -ttctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccct -cccatccatccatcctcccatccatccacccttccatccatccatccacccacccttcca -tccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcct -cccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatcca -tccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatcca -tccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctccca -tcctc----ccatccatccatccatccatccatcctcccatcctcccatcctcccatcca -tcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccca -tccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcca -tccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccg -tgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaa -aaatgaaaaaaagaatatattgatttcaggccagttacataga ->p:HG002_2_chr20:60314229-60315121 -cacttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgca -cacctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctg -tcctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccat -ccatttgtccttccttccttccttccttccttc---cttccttccttccttccttccttc -cttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaac -catcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatc -catccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatc -catcctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatc -cactcttccatccatccatccacccaccctt----------------ccatccatccatc -ctcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatc -catcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatc -ctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatccatc -ctcccatcctcccatccatccatccatcctcccatccgtccatccatccttccatccac- ----------------cctcccatccatccatcctcccatccatctaccctcccatccatc -catcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatc -tatccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcc -tcccataatctatcttcccatccatttgtccttccttccttccttccttccttccttcct -tcgttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccaccca -accatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatcta -tccat--------------------ccatcctcccatccatcctcccatcctcccatcca -ttctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccct -cccatccatccatcctcccatccatccacccttccatccatccatccacccacccttcca -tccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcct -cccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatcca -tccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatcca -tccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctccca -tcctcccatccatccatccatccatccatccatcctcccatcctcccatcctcccatcca -tcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccca -tccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcca -tccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccg -tgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaa -aaatgaaaaaaagaatatattgatttcaggccagttacataga ->ref_chr20:60314229-60315121 -cacttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgca -cacctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctg -tcctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccat -ccatttgtccttccttccttccttccttccttccttcttccttccttccttccttccttc -cttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaac -catcctcccatccatcctcacatcgatcttcgcatccatccatcgatcgatctatccatc -catccattc----------------------------tcccattcatccatcctcccatc -catcctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatc -cacccttccatccatccatccacccaccctt----------------ccatccatccacc -ctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcctcc -cat--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------ccatccatccatccatccatccatcctcccatcctcccatcctcccatcca -tcgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctccca -tccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgcca -tccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccg -tgagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaa -aaatgaaaaaaagaatatattgatttcaggccagttacataga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_02ac508769a0aaa6badcfe17113fdd30.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_02ac508769a0aaa6badcfe17113fdd30.msa deleted file mode 100644 index 3b29d8fd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_02ac508769a0aaa6badcfe17113fdd30.msa +++ /dev/null @@ -1,45 +0,0 @@ ->syndip_1_chr20:63154577-63155031 -gtgggggtgtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttg -cccccgtccttccttctccctcctcccttcctcctccctcctcttccctccc-------- ---------------------------------------------tcctgcttcctccctc -tgccctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctc -ccttcctcctcctcccccctttcccaccctcctccccctttccctccctcctcccgactc -cctctccccttctccctcttctca---------------------tcccttcctcctcct -ccctccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtccta -gcccatatccaagggcctgtctcagctacaaagtt ->syndip_2_chr20:63154577-63155031 -gtgggggtgtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttg -cccccgtccttccttctccctcctcccttcctcctccctcctcttccctccctcctgctt -cctccctctgccctccctcctccctcttcctccctcctcctccttcctgcttcctccctc -tgccctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctc -ccttcctcctcctcccccctttcccaccctcctccccctttccctccctcctcccgactc -cctctccccttctccctcttctcatcccttcctcctcctccctcctcccttcctcctcct -ccctccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtccta -gcccatatccaagggcctgtctcagctacaaagtt ->p:HG002_1_chr20:63154577-63155031 -gtgggggtgtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttg -cccccgtccttccttctccctcctcccttcctcctccctcctcttccctccctcctgctt -cctccctctgccctccctcctccctcttcctccctcctcctccttcctgcttcctccctc -tgccctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctc -ccttcctcctcctcccccctttcccaccctcctccccctttccctccctcctcccgactc -cctctccccttctccctcttctcatcccttcctcctcctccctcctcccttcctcctcct -ccctccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtccta -gcccatatccaagggcctgtctcagctacaaagtt ->p:HG002_2_chr20:63154577-63155031 -gtgggggtgtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttg -cccccgtccttccttctccctcctcccttcctcctccctcctcttccctccctcctgctt -cctccctctgccctccctcctccctcttcctccctcctcctccttcctgcttcctccctc -tgccctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctc -ccttcctcctcctcccccctt--------------------------------------- -----------------------------------ctcctccctcctcccttcctcctcct -ccctccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtccta -gcccatatccaagggcctgtctcagctacaaagtt ->ref_chr20:63154577-63155031 -gtgggggtgtggatcaggcctgatctcccctagtctcctcctgcaatgcccagattcttg -cccccgtccttccttctccctcctcccttcctcctccctcctcttccctccctcctgctt -cctccctctgccctccctcctccctcttcctccctcctcctccttcctgcttcctccctc -tgccctccctcctccctcttcctccctcctcctcccctctcctctttcctcctccctctc -ccttcctcctcctcccccctttcccaccctcctccccctttccctccctcctcccgactc -cctctccccttctccctcttctcatcccttcctcctcctccctcctcccttcctcctcct -ccctccttcctccctcctccctcctccccacactgtccatttgcaggctgcctggtccta -gcccatatccaagggcctgtctcagctacaaagtt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_044d295f667d84ae550fa2608e24e03f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_044d295f667d84ae550fa2608e24e03f.msa deleted file mode 100644 index fb22cdd6..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_044d295f667d84ae550fa2608e24e03f.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:57948891-57949456 -tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg -gattaatggatggatgaatggatgatggatggatgaatgagatggatggatt-------- ---------gatggatggatggatggatggatggatggaagaatggatgatggatggatga ---------------------gatggatggatggatggatggaagaatggatgatggatgg -atga--------gatggatggatggatggggggttggatggatggatgg----------- --------------------------------------------atggatggatggatagt -ggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatgg -atggatgaatgagatggatggatt------------gatggatggatggatggatggaag -aatggatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatg -gatggatggatggatggcagatggat ->syndip_2_chr20:57948891-57949456 -tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg -gattaatggatggatgaatggatgatggatggatgaatgagatggatggattgatggatg -gatggatggatggatggatggatggatggatggatggaagaatggatgatggatggatga -gatggatggatggatggatggatggatggatggatggatggaagaatggatgatggatgg -atgagatggatggatggatggatggatggggggttggatggatggatggatggatggatg -gatagtggatagatggatgaatagtgaatggataaatggattaatggatggatggatagt -ggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatgg -atggatgaatgagatggatggattgatggatggatggatggatggatggatggatggaag -aatggatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatg -gatggatggatggatggcagatggat ->p:HG002_1_chr20:57948891-57949456 -tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg -gattaatggatggatgaatggatgatggatggatgaatgagatggatggattgatggatg -gatggatggatggatggatggatggatggatggatggaagaatggatgatggatggatga -gatggatggatggatggatggatggatggatggatggatggaagaatggatgatggatgg -atgagatggatggatggatggatggatggggggttggatggatggatggatggatggatg -gatagtggatagatggatgaatagtgaatggataaatggattaatggatggatggatagt -ggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatgg -atggatgaatgagatggatggattgatggatggatggatggatggatggatggatggaag -aatggatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatg -gatggatggatggatggcagatggat ->p:HG002_2_chr20:57948891-57949456 -tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg -gattaatggatggatgaatggatgatggatggatgaatgagatggatggattgatggatg -gatggatggatggatggatggatggatggatggatggaaga------------------- ------------------atggatggatggatggatggatggaagaatggatgatggatgg -atgagatggatggatggatggatggatggggggttggatggatggatggatggatggatg -gatagtggatagatggatgaatagtgaatggataaatggattaatggatggatggatagt -ggatagatg--tgatggatggatggatggatggatggatggatggaagaatggatgatgg -atggatgaatgagatgggtggattgatggatggatggatggatggatggatggatgga-- ------------------------------------------------------------- -----------tggatggcagatggat ->ref_chr20:57948891-57949456 -tggatggatggatggatggatggatagtggatagatggatgaatagtggatggataaatg -gattaatggatggatgaatggatgatggatggatgaatgagatggatggattgatggatg -gatggatggatggatggatggatggatggatggatggaagaatggatgatggatggatga -gatggatggatggatggatggatggatggatggatggatggaagaatggatgatggatgg -atgagatggatggatggatggatggatggggggttggatggatggatggatggatggatg -gatagtggatagatggatgaatagtgaatggataaatggattaatggatggatggatagt -ggatagatggatgaatagtggatggataaatggattaatggatggatgaatggatgatgg -atggatgaatgagatggatggattgatggatggatggatggatggatggatggatggaag -aatggatgatggatggatgaatgagatgggtggattgatggatggatggatggatggatg -gatggatggatggatggcagatggat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_07f1095434eca0d354088c9d9ca44ce0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_07f1095434eca0d354088c9d9ca44ce0.msa deleted file mode 100644 index 3e38acbf..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_07f1095434eca0d354088c9d9ca44ce0.msa +++ /dev/null @@ -1,250 +0,0 @@ ->syndip_1_chr20:62057492-62058878 -aacaccaccctacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgc -cttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaaga -cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctc-gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggaca -caggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca -cagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcc -tacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagg -acggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaa -gacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaac -ctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgggg -ctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcc -acagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggc -ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctcagc -aagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggg -ggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagac -aatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacaca -ccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggac -acaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaa -cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacagtggg -gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg -ccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacagg -tctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagga -aggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctca -gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaag -acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa -tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctc-gggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcc -acagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggac ->syndip_2_chr20:62057492-62058878 -aacaccaccctacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgc -cttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-gggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctc-gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctc-gggggccaacctcagcaagacctcaggaaggacggaca -caggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctc-gggggccaacc -tcagcaagacctcaggaaggacggac---------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------ ->p:HG002_1_chr20:62057492-62058878 -aacaccaccctacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgc -cttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc-gggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacacc -aggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggaca -caggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctc-gggggccaacc -tcagcaagacctcaggaaggacggac---------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------ ->p:HG002_2_chr20:62057492-62058878 -aacaccaccctacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgc -cttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaaga -cctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggc -caacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaat -ggggctc-gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggaca -caggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc -tcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggc -tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca -cagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcc -tacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagg -acggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaa -gacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaac -ctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgggg -ctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcc -acagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggc -ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctcagc -aagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggg -ggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagac -aatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacaca -ccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggac -acaggcctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaa -cctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggg -gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg -ccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacagg -tctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagga -aggacggacacaggcctacacaccaggccacagacaatggggctc-gggggccaacctca -gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctc-gggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc -tcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggc -tc-gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcc -acagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggac ->ref_chr20:62057492-62058878 -aacaccaccctacctggctacgctcctctcacaactttgagatcaagatgccacgtgtgc -cttcctcacatcggcgctttccagtgatgcccagtgggggacacaaagggcccagcaaga -cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacacc -aggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggaca -caggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctca -ggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaacc -tcagcaagacctcaggaaggacggac---------------------------------- ------------------------------------------------------------- ------------------------------------------------------acaggcc -tacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagg -acggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaa -gacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaac -ctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgggg -ctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcc -acagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggc -ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctcagc -aagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggg -ggccaacctcagcaagacctcaggaaggacggac-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_092810086934f7787bd8bd7029125238.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_092810086934f7787bd8bd7029125238.msa deleted file mode 100644 index 14b2ec66..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_092810086934f7787bd8bd7029125238.msa +++ /dev/null @@ -1,225 +0,0 @@ ->syndip_1_chr20:38463887-38464454 -tatatatatatactgtcatatatatattttatatatatatactgtcatatatatatttta -tatatatactgtcatatgtatattttatatatatactgtcatatgtatattt--tatata -tatactgttatatgtatattttatatatatatactgttatatatatatttt-tatatata -tactgttatatatatttttttatatatatactgttatatatat----------------- -------------ttttatatatatactgttatatatatattttatatatatactgttata -tatatattttatatatactgttatatatatatattttatatatatactgttatatataat -ttttttcatatatatactgttatatatatattttatatatatatactgttatatatatat -tttatatatatactgttatatatatatattttatatatatactgttattttttatatata -tactgttatatatatattttatatatatactgttatatatatattatctatatactgtta -tgtgtatattttatctatatactgttatgtgtatattttatctatatactgttatgtgta -tattttacctatatacttttatgtgtatattttatatatatactgttatgtgtatatttt -atatatatactgttatgtgtatattttttatatatactgttatgtgtatattttatatat -atatactgttatgtgtatattttatatatatatactgttatgtgtatattttatatatat -actgttatgtgtatattttatatatatactgttatatatagttcatatatatactgttat -atgtatagttcatatatatactgttatatatatagttcatatgtatactgttatatatat -agttcatatatatactgttatatatatagttcatatatatactgttatatatatatagtt -catatatatactgttatatatagttcatatatatactgttatatatatagttcatatata -tactgttatatatatagttcatatatatactgttatatatagttcatatatatatactgt -tctatatatagttcatatatatatactgttatatatatagttcatatatatatactgtta -tatatagttcatatatatatagttcatatatatactgttatatatatagttcatatatat -actgttatatacatagttcatatatatactgttatatatatagttcatatatatatactg -ttatatatatagttcatatatatactgttgtatatagttcatatatatactgttatatat -atagttcatatattactgttatatatatagttcatatatatactgttatatatatatagt -tcatatatatactgttatatatagtttatatatatatactgttatatatatagtttatat -atatatactgttatatatatagtttatatatatatactgttatatatatatagtttatat -atatatactgttatatatatagtttatatatatatactgttatatatatatagtttatat -atactgttatatatatagtttatatatatactgttatatatatagtttatatatatactg -ttatatatatagtttatatatatactgttatatatatagtttatatatatactgttatat -atatagtttatatatatactgttatatatatagtttatatatatactgttatatatatag -tttatatatatatactgt--tatatatagtttatatatactgttatatatatagtttata -tactgttatatatagtttatatatatatactgttatatatagtttatatatatatactgt -tatatatatatagtttatatatatatactgttatatatatatagtttatatatatactgt -tatatatatatagtttatatatatactgttgtatatatagtttatatatatactgttata -tatatatttgtgtatatatactgttatataaatatatttgtgtatatatactgttatata -tatattttatgtatatatactgttatatatatattttatgtatatatactgttatatata -tattttatgtatatatactgttatatatatattttatgtatatatactgttatatatata -ttttatgtatatatactgttatatatattttatgtatatatactgttatatatat-ttta -tgtatatatactgttatatatatattttatgtatatatactgttatatctgtatatttta -tgtttatatactgttatatctgtatattttatgtatatatactgttatatctgtatattt -tatgtatatactgttatatagatactgttatatatatactgatatatatactgttatata -tatactgatatatatatactgttatatatatactgttatatatatatactgttacatata -catatatatactgttatatatatactgttatatatattgttatatatatacacatatata -tatacatatatatatacatatatatatacatatatatatacatatatatatacacgtata -tatatacatatatatatacacatatatatatatacacacacatatatatatat ->syndip_2_chr20:38463887-38464454 -tatatatatatactgtcatatatatattttatatatatatactgtcatatatatatttta -tatatatactgtcatatgtatattttatatatatactgtcatatgtatattttatatata -tatactgttatatatatattttatatatatatactgttatatgtatattttatatatata -tactgttatatatatatttttatatatatactgttatatatatttttttatatatatact -gttatatatat-ttttatatatatactgttatatatatattttatatatatactgttata -tatatattttatatatactgttatatatatatattttatatatatactgttatatataat -ttttttcatatatatactgttatatatatattttatatatatatactgttatatatatat -tttatatatatactgttatatatatatattttatatatatactgttattttttatatata -tactgttatatatatattttatatatatactgttatatatatattatctatatactgtta -tgtgtatattttatctatatactgttatgtgtatattttatctatatactgttatgtgta -tattttacctatatacttttatgtgtatattttatatatatactgttatgtgtatatttt -atatatatactgttatgtgtatattttttatatatactgttatgtgtatattttatatat -atatactgttatgtgtatattttatatatatatactgttatgtgtatattttatatatat -actgttatgtgtatattttatatatatactgttatatatagttcatatatatactgttat -atgtatagttcatatatatactgttatatatatagttcatatgtatactgttatatatat -agttcatatatatactgttatatatatagttcatatatatactgttatatatatatagtt -catatatatactgttatatatagttcatatatatactgttatatatatagttcatatata -tactgttatatatatagttcatatatatactgttatatatagttcatatatatatactgt -tctatatatagttcatatatatatactgttatatatatagttcatatatatatactgtta -tatatagttcatatatatatagttcatatatatactgttatatatatagttcatatatat -actgttatatacatagttcatatatatactgttatatatatagttcatatatatatactg -ttatatatatagttcatatatatactgttgtatatagttcatatatatactgttatatat -atagttcatatattactgttatatatatagttcatatatatactgttatatatatatagt -tcatatatatactgttatatatagtttatatatatatactgttatatatatagtttatat -atatatactgttatatatatagtttatatatatatactgttatatatatatagtttatat -atatatactgttatatatatagtttatatatatatactgt--tatatatatagtttatat -atactgtta-------------------------tatatatatagtttatatatatactg -ttatatatatagtttatatatatactgttatatatatagtttatatatatactgttatat -atatagtttatatatatactgttatatatatagtttatatatatactgttatatatatag -tttatatatatatactgttatatatatagtttataaatactgttatatatatagtttata -tactgttatatatagtttatatatatatactgttatatatagtttatatatatatactgt -tatatatatatagtttatatatatatactgttatatatatatagtttatatatatactgt -tatatatatatagtttatatatatactgttgtatatatagtttatatatatactgttata -tatatatttgtgtatatatactgttatataaatatatttgtgtatatatactgttatata -tatattttatgtatatatactgttatatatatattttatgtatatatactgttatatata -tattttatgtatatatactgttatatatatattttatgtatatatactgtta-------- --------------------tatatatattttatgtatatatactgttatatatat-ttta -tgtatatatactgttatatatatattttatgtatatatactgttatatctgtatatttta -tgtttatatactgttatatctgtatattttatgtatatatactgttatatctgtatattt -tatgtatatactgttatatagatactgttatatatatactgatatatatactgttatata -tatactgatatatatatactgttatatatatactgttatatatatatactgttacatata -catatatatactgttatatatatactgttatatatattgttatatatatac--------- ----acatatatatatacatatatatatacatatatatatacatatatatatacacgtata -tatatacatatatatatacacatatatatatatacacacacatatatatatat ->p:HG002_1_chr20:38463887-38464454 -tatatatatatactgtcatatatatattttatatatatatactgtcatatatatatttta -tatatatactgtcatatgtatattttatatatatactgtcatatgtatattt--tatata -tatactgttatatgtatattttatatatatatactgttatatatatatttt-tatatata -tactgttatatatatttttttatatatatactgttatatatat--ttttatatatatact -gttatatatatattttatatatatactgttatatatatattttatatatatactgttata -tatatattttatatatactgttatatatatatattttatatatatactgttatatataat -ttttttcatatatatactgttatatatatattttatatatatatactgttatatatatat -tttatatatatactgttatatatatatattttatatatatactgttattttttatatata -tactgttatatatatattttatatatatactgttatatatatattatctatatactgtta -tgtgtatattttatctatatactgttatgtgtatattttatctatatactgttatgtgta -tattttacctatatacttttatgtgtatattttatatatatactgttatgtgtatatttt -atatatatactgttatgtgtatattttttatatatactgttatgtgtatattttatatat -atatactgttatgtgtatattttatatatatatactgttatgtgtatattttatatatat -actgttatgtgtatattttatatatatactgttatatatagttcatatatatactgttat -atgtatagttcatatatatactgttatatatatagttcatatgtatactgttatatatat -agttcatatatatactgttatatatatagttcatatatatactgttatatatatatagtt -catatatatactgttatatatagttcatatatatactgttatatatatagttcatatata -tactgttatatatatagttcatatatatactgttatatatagttcatatatatatactgt -tctatatatagttcatatatatatactgttatatatatagttcatatatatatactgtta -tatatagttcatatatatatagttcatatatatactgttatatatatagttcatatatat -actgttatatacatagttcatatatatactgttatatatatagttcatatatatatactg -ttatatatatagttcatatatatactgttgtatatagttcatatatatactgttatatat -atagttcatatattactgttatatatatagttcatatatatactgttatatatatatagt -tcatatatatactgttatatatagtttatatatatatactgttatatatatagtttatat -atatatactgttatatatatagtttatatatatatactgttatatatatatagtttatat -atatatactgttatatatatagtttatatatatatactgt--tatatatatagtttatat -atactgtta-------------------------tatatatatagtttatatatatactg -ttatatatatagtttatatatatactgttatatatatagtttatatatatactgttatat -atatagtttatatatatactgttatatatatagtttatatatatactgttatatatatag -tttatatatatatactgttatatatatagtttataaatactgttatatatatagtttata -tactgttatatatagtttatatatatatactgttatatatagtttatatatatatactgt -tatatatatatagtttatatatatatactgttatatatatatagtttatatatatactgt -tatatatatatagtttatatatatactgttgtatatatagtttatatatatactgttata -tatatatttgtgtatatatactgttatataaatatatttgtgtatatatactgttatata -tatattttatgtatatatactgttatatatatattttatgtatatatactgttatatata -tattttatgtatatatactgttatatatatattttatgtatatatactgtta-------- --------------------tatatatattttatgtatatatactgttatatatat-ttta -tgtatatatactgttatatatatattttatgtatatatactgttatatctgtatatttta -tgtttatatactgttatatctgtatattttatgtatatatactgttatatctgtat---- -----------ctgttatatagatactgttatatatatactgatatatatactgttatata -tatactgatatatatatactgttatatatatactgttatatatatatactgttacatata -catatatatactgttatatatatactgttatatatattgttatatatatacacatatata -tatacatatatatatacatatatatatacatatatatatacatatatatatacacgtata -tatatacatatatatatacacatatatatatatacacacacatatatatatat ->p:HG002_2_chr20:38463887-38464454 -tatatatatatactgtcatatatatattttatatatatatactgtcatatatatatttta -tatatatactgtcatatgtatattttatatatatactgtcatatgtatattt--tatata -tatactgttatatgtatattttatatatatatactgttatatatatatttt-tatatata -tactgttatatatatttttttatatatatactgttatatatat----------------- -------------ttttatatatatactgttatatatatattttatatatatactgttata -tatatattttatatatactgttatatatatatattttatatatatactgttatatataat -ttttttcatatatatactgttatatatatattttatatatatatactgttatatatatat -tttatatatatactgttatatatatatattttatatatatactgttattttttatatata -tactgttatatatatattttatatatatactgttatatatatattatctatatactgtta -tgtgtatattttatctatatactgttatgtgtatattttatctatatactgttatgtgta -tattttacctatatacttttatgtgtatattttatatatatactgttatgtgtatatttt -atatatatactgttatgtgtatattttttatatatactgttatgtgtatattttatatat -atatactgttatgtgtatattttatatatatatactgttatgtgtatattttatatatat -actgttatgtgtatattttatatatatactgttatatatagttcatatatatactgttat -atgtatagttcatatatatactgttatatatatagttcatatgtatactgttatatatat -agttcatatatatactgttatatatatagttcatatatatactgttatatatatatagtt -catatatatactgttatatatagttcatatatatactgttatatatatagttcatatata -tactgttatatatatagttcatatatatactgttatatatagttcatatatatatactgt -tctatatatagttcatatatatatactgttatatatatagttcatatatatatactgtta -tatatagttcatatatatatagttcatatatatactgttatatatatagttcatatatat -actgttatatacatagttcatatatatactgttatatatatagttcatatatatatactg -ttatatatatagttcatatatatactgttgtatatagttcatatatatactgttatatat -atagttcatatattactgttatatatatagttcatatatatactgttatatatatatagt -tcatatatatactgttatatatagtttatatatatatactgttatatatatagtttatat -atatatactgttatatatatagtttatatatatatactgttatatatatatagtttatat -atatatactgttatatatatagtttatatatatatactgttatatatatatagtttatat -atactgttatatatatagtttatatatatactgttatatatatagtttatatatatactg -ttatatatatagtttatatatatactgttatatatatagtttatatatatactgttatat -atatagtttatatatatactgttatatatatagtttatatatatactgttatatatatag -tttatatatatatactgt--tatatatagtttatatatactgttatatatatagtttata -tactgttatatatagtttatatatatatactgttatatatagtttatatatatatactgt -tatatatatatagtttatatatatatactgttatatatatatagtttatatatatactgt -tatatatatatagtttatatatatactgttgtatatatagtttatatatatactgttata -tatatatttgtgtatatatactgttatataaatatatttgtgtatatatactgttatata -tatattttatgtatatatactgttatatatatattttatgtatatatactgttatatata -tattttatgtatatatactgttatatatatattttatgtatatatactgttatatatata -ttttatgtatatatactgttatatatattttatgtatatatactgttatatatat-ttta -tgtatatatactgttatatatatattttatgtatatatactgttatatctgtatatttta -tgtttatatactgttatatctgtatattttatgtatatatactgttatatctgtatattt -tatgtatatactgttatatagatactgttatatatatactgatatatatactgttatata -tatactgatatatatatactgttatatatatactgttatatatatatactgttacatata -catatatatactgttatatatatactgttatatatattgttatatatatacacatatata -tatacatatatatatacatatatatatacatatatatatacatatatatatacacgtata -tatatacatatatatatacacatatatatatatacacacacatatatatatat ->ref_chr20:38463887-38464454 ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------tatatatatatactgtcatata -tatattttatatatatatactgtcatatatatatttta--tatatatactgtcatatgta -tatttta--tatatatactgtcatatgtatatttta--tatatatactgtta-------- --------------------tatgtatattttatatatatatactgttatatatatatttt -tatatatatactgttatatatat-ttttttatatatatactgttatatata-----tttt -tatatatatactgttata----tatatattttatatatatactgttata----tatatat -tttatatatactgttatatagatactgttatatatatactgatatatatactgttatata -tatactgatatatatatactgttatatatatactgttatatatatatactgttacatata -catatatatactgttatatatatactgttatatatattgttatatatatacacatatata -tatacatatatatatacatatatatatacatatatatatacatatatatatacacgtata -tatatacatatatatatacacatatatatatatacacacacatatatatatat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0c3e8d54fa39f3242fb2b7e97c637b37.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0c3e8d54fa39f3242fb2b7e97c637b37.msa deleted file mode 100644 index 6540c54c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0c3e8d54fa39f3242fb2b7e97c637b37.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:61282815-61283589 -tggtgtgcacgtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgt--- ------------------------------------------------------------- -----------------------------------------------------gtgtgatg -tacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgt -gctgtggcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc--gtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgc--- ------------tgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgt -gtgatgtacgtgcgtttgcacgcgtgtgctgtg--gtgtgtgatgtacgtgcgtttgcac -gcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtg -atgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcg -cgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatg -tacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgt -gctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgt -gtgcgtttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgtttgcacgcgtgtgct -gtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtg -cgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgc---- --tgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttac -acgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtg ->syndip_2_chr20:61282815-61283589 -tggtgtgcacgtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtg -tgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacg -cgtgtgctgt-gtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatg -tacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgt -gctgtggcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc--gtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgt -ggcgtgtgtgatgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgt -gtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcac -gcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtg -atgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcg -cgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatg -tgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgt -gctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgt -gtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgct -gtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtg -cgtttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtg -gtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttac -acgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtg ->p:HG002_1_chr20:61282815-61283589 -tggtgtgcacgtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtg -tgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacg -cgtgtgctgtggcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc--gtgtgatg -tacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgt -gctgtggcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgt -ggcgtgtgtgatgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgt -gtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcac -gcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtg -atgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcg -cgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatg -tgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgt -gctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgt -gtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgct -gtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtg -cgtttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtg -gtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttac -acgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtg ->p:HG002_2_chr20:61282815-61283589 -tggtgtgcacgtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgt--- ------------------------------------------------------------- -----------------------------------------------------gtgtgatg -tacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgt -gctgtggcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc--gtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgc--- ------------tgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgt -gtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcac -gcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtg -atgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcg -cgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatg -tacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgt -gctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgt -gtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgct -gtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtg -cgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgc---- --tgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttac -acgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtg ->ref_chr20:61282815-61283589 -tggtgtgcacgtgtgtgc------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------gtgtgatgcatgt -gcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtgcatttgcacgcgtgtgc--- ------------tgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggc--gt -gtgatgtacgtgcgtttgcacgcgcgtgctgtggc--gtgtgatgtacgtgcgtttgcac -gcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtg -atgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcg -cgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatg -tacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgt -gctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtac -gtgcgtttgcacgcgcgtgctgtggc---------gtgtgtgcgtttgcacgcgcgtgct -gtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtg -cgtttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtg -gtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttac -acgcgtgtgctgtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0c8572a4abbd43dfe7727d1bbe104e58.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0c8572a4abbd43dfe7727d1bbe104e58.msa deleted file mode 100644 index 68732c67..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0c8572a4abbd43dfe7727d1bbe104e58.msa +++ /dev/null @@ -1,225 +0,0 @@ ->syndip_1_chr20:16257641-16259445 -ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa -gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata -cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat -cccaaagagacacaccccttccccatcccaaagagacacaccccttccccatcccaaaca -cacacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc -cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct -tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc -acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc -cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc -atcccaaacacacccaccctttcctgcatcccaaacacccacaccccttccccatcccaa -acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca -ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc -cccatcacaaacacacg--------------------------caccccttccccatccc -aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca -caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc -ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat -tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac -gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc -cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc -tcaaatacacgcaacccttccccatcccaaacacacacacctattccccatccgaaacac -acacaccccttcctcatcccacacacacccattccccatcccagacacacccatcccttc -cccatactaaacacaaccaccccttccccatcccacacacacacaccccttccccaattc -caaacacacacaccccttccccattcaaaacacacgcaccccttcccatctgaaacacac -ccactccttcccatctgaaacacacccactccttcccatcccaaacacacccactccttc -ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca -aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac -ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc -ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc -caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac -ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc -ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat -cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac -acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc -cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat -cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca -cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt -tcccatcccagacacatccaccccttccacaactctgaacacccaccccttccccatccc -aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac -acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct -tccccatcccaaacacacacaca-------------------------ccttccccatcc -caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata -cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact -cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg -gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaa ->syndip_2_chr20:16257641-16259445 -ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa -gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata -cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat -cccaaagagacacaccccttccccatcccaaagag------------------------- --acacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc -cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct -tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc -acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc -cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc -atcccaaacacacccaccctttcctgcatcccaaacacacacaccccttccccatcccaa -acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca -ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc -cccatcacaaacacacgcaccccttccccatcccaaacatacacaccccttccccatccc -aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca -caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc -ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat -tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac -gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc -cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc -tcaaatacacgcaacccttc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------c -ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca -aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac -ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc -ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc -caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac -ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc -ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat -cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac -acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc -cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat -cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca -cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt -tcccatcccagacacatccaccccttccacaactccgaacacccaccccttccccatccc -aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac -acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct -tccccatcccaaacacacacacaccttcccatcccaaacacacacaccccttccccatcc -caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata -cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact -cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg -gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaa ->p:HG002_1_chr20:16257641-16259445 -ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa -gtctgtttctaagcagcagcctgatggatccatttttataatctgaaatcagatatcata -cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat -cccaaagagacacaccccttccccatcccaaagag------------------------- --acacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc -cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct -tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc -acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc -cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc -atcccaaacacacccaccctttcctgcatcccaaacacacacaccccttccccatcccaa -acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca -ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc -cccatcacaaacacacgcaccccttccccatcccaaacatacacaccccttccccatccc -aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca -caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc -ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat -tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac -gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc -cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc -tcaaatacacgcaacccttc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------c -ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca -aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac -ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc -ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc -caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac -ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc -ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat -cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac -acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc -cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat -cccaaacacacacccattccccatcccagacacacccacccgttccccatc--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------- ->p:HG002_2_chr20:16257641-16259445 -ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa -gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata -cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat -cccaaagagacacaccccttccccatcccaaagagacacaccccttccccatcccaaaca -cacacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc -cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttccct -tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc -acacacaccttccacttcccaaacacacacaccccttccccatcccaaacacacacaacc -cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc -atcccaaacacacccaccctttcctgcatcccaaacacccacaccccttccccatcccaa -acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca -ccccttccacatcagaaacacacacaccccttctcatcccaaacacaaacacacccattc -cccatcacaaacacacg--------------------------caccccttccccatccc -aaacacacacaccccttccccaattctaaacacacacaccccttccccatcccaaacaca -caccccccttccccatcccaaacacacaccccccttccccatcccaaacacacccacccc -ttcccacatcccaaacacacacaccccttccctatcccaaacacacactccatccccaat -tccaaacacacacaccccttccccatcccaaacacacacaccccttcccccatcccaaac -gcacacaccccttccctatcccaaacacacaccccttccctttccaaaacacacccatcc -cttccccatcccaaacacacacaacccttcccatcccagacacacccaccccttcccatc -tcaaatacacgcaacccttccccatcccaaacacacacacctattccccatccgaaacac -acacaccccttcctcatcccacacacacccattccccatcccagacacacccatcccttc -cccatactaaacacaaccaccccttccccatcccacacacacacaccccttccccaattc -caaacacacacaccccttccccattcaaaacacacgcaccccttcccatctgaaacacac -ccactccttcccatctgaaacacacccactccttcccatcccaaacacacccactccttc -ccatcccaaacacacacaccccttccccatcccaaaaacacacaccctttcgcaatccca -aatacacaagccccttcccaaattccacacacacacacctcttccccatcccaaacaaac -ccaccctttccccattcgaaacacacacaccccttctccaattccaaacacacacacccc -ttcccatctcaaacacacggacaccttccacatcccaaatacacacaccccttcccatcc -caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac -ccccaccccttcccatccccaaaacacacacccctttcccatcccaaatacacaaacccc -ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat -cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac -acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc -cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat -cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca -cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt -tcccatcccagacacatccaccccttccacaactctgaacacccaccccttccccatccc -aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac -acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct -tccccatcccaaacacacacaca-------------------------ccttccccatcc -caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata -cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact -cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg -gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaa ->ref_chr20:16257641-16259445 -ctgagattcctgccacctttgccccttacttttctcaccccgttcactgagggccctcaa -gtctgtttctaagcagcagcctgagggatccatttttataatctgaaatcagatatcata -cccacaccccaaaacacacacactccttccccatcccaaagagacacaccccttccccat -cccaaagagacacaccccttccccatcccaaagagacacaccccttccccatcccaaaca -cacacaccccttccccatcccaaacacacacaccccttccccatcccaaacacacacacc -cctttcccatcccaaacacacacacccattgcccatcctaaacacacacacaccttgcct -tcgcaaacacacacaccccttccccatcacaaacacacacaccctttccctatcccatgc -acacacaccttccacttcccaaacacacacaccccttccccatgccaaacacacacaacc -cttccccaattctaaacacacacacctcttccccatcccaaacacaaacaccccttcccc -atcccaaacacacccaccctttcctgcatgccaaacacccacaccccttccccatcccaa -acacacaccccatccccaattccaaacacacacaccccttccccatcccaaacacacaca -ccccttccacatgagaaacacacacaccccttctcatcccaaacacaaacacacccattc -cccatcacaaacacacg--------------------------caccccttccccatccc -aaacacacacaccccttccccaattgt--------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------aaacacacacaccccttctccaattccaaacacacacacccc -ttcccatcacaaacacacacacaccttccacatcccaaatacacacaccccttcccatct -caaacacacacatcccttccccaattccaaaaacacacaccccttccccatcccaaacac -ccccaccccttcccatcccc-aaacacacacccctttcccatcccaaatacacaaacccc -ttccctaattccacacacacacaccccttccccatcccaaacacacataccccttcccat -cccaaagacacacactcattctgcatcccaaacacacacaccccttcccatcccaaacac -acacactacctccgcatcccaaacacatataccccttccccatcccaaacacatacaccc -cttccccatcgccaacacacacaccccttccccatcccaaacacacacacccctttccat -cccaaacacacacccattccccatcccagacacacccacccgttccccatcccagacaca -cacaacccttccccaattccaaacacacaccccttcccatcccaaacacacacacccatt -tcccatcccagacacatccaccccttccacaactctgaacacccaccccttccccatccc -aaacacacacaccccttccccatcccaaacacacacacccattccccatcccaaacacac -acacccattccccatcccaaacacaaccaccccttccccatcccaaacacacacacccct -tccccatcccaaacacacacaca-------------------------ccttccccatcc -caaacacacccacccttactccatctcaaacatgtacaccccttcccctatcccaaaata -cacacatccatccctacacaccctcacccatttccccatcccagaacctatgcaccaact -cagtttatttgaacatgccaggcactgaactaagagaaccaaagtagcaggaggaatacg -gtgttgtcctcccagaacttaccccctgcacgggagtcagccagggaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0cc1357e1d86aa9f6afd24f35da9b52d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0cc1357e1d86aa9f6afd24f35da9b52d.msa deleted file mode 100644 index 91059801..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0cc1357e1d86aa9f6afd24f35da9b52d.msa +++ /dev/null @@ -1,125 +0,0 @@ ->syndip_1_chr20:8661834-8662229 -taacttcagtatttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacc -cagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatata -attatataattatttattatataattatatataattatataattatttattatataatta -tatataattatataattatttattatataattatatataa-tatacaattatttattata -taattatatataattatatatttattatatttat-----tatacagttatataataaata -attatataattatatataattatat-atatataattatatataattatatataattatat -aattatatataattg-tatataattatttattatataattatatatta-tttattat--a -taattatataattatatat-----tatttattatatattatataatt------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------atataattatatattatttattatata-----atatataattatatat---- ----tatttattatataattatatattatttatta---------tatatattatttattat -ata----------------------attatatattatgtattatataattatataattat -atattatgtattatataat----------------tatatattatgtattatataattat -ataattatatattatgtattatataattatatattatttattatataattatataattat -atattatttattatataattatataattatatattatttattatataat----------- -----------tatataattatatattatttattatataattatataattatatattattt ---------attatataattatatattatttattatataattatatattatttattacata -aatatatattatttattacataagtatatatcacttattatataattgcatataattatt -tattatataattgcatataa----ttattatataattgtatatagttatttattatataa -ttg-------------------------tatatagttatttattatataattctatata- -------attatttattatctaattctatattaaatataattatttattatctaattctat -attatatataattatttattatataattctatattatatataattattatataatt ->syndip_2_chr20:8661834-8662229 -taacttcagtatttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacc -cagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatata -attatataattatttattatataattatatataattatat-------------------- --------------aattatttattatataatgatatataattatataattatttattata -taattatatataattatataattatttattatataattatatataattatataattattt -attatataattatatataattatataattatttattatataattatat------------ ------------ataattatataattatttattatataattatatataattatataattat -ttattatataattatatataattatataattatt-tattatataattatatataattata -taattatttattatataattatatataattatataattatttattatataattatatata -atatacaattatttattatataattatatataatatacaattatttattatataattata -tataattatatatttattatatttattatacagttatataataaataattatataattat -atataattatataattatatataattatatatatataattatatgtaattatatataatt -atataattattatataattgtatataatatataattatataattatatattatttattat -ataatatataattatataattatatattatttattatataatatataattatataattat -atattatttattatataattatatattatttattatatatattatttattatataattat -ataattatatattatttattatataattatatattatttattatataa-tatataattat -atattatttattatataa-tatataattatatattatttattatataattatatattatg -tattatataatatataattatatattatgtattatataattatataattatatattattt -attatataattatataattatatattatttattacataattatatattatttattacata -agtatatattatttattacataagtatatatcacttattatataattgtatataattatt -tattatataattgcatataattatttattatataattgtatatagttatttattatataa -ttctatatagttatttattatataattctatataattatttattatctaattctatatta -tatataattatttattatctaattctatattaaatataattatttattatctaattctat -attatatataattatttattatataattctatattatatataattattatataatt ->p:HG002_1_chr20:8661834-8662229 -taacttcagtatttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacc -cagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatata -attatataattatttattatataattatatataattatat-------------------- --------------aattatttattatataattatatataa-tatacaattatttattata -taattatatataattatatatttatttattatataattatatataattatataattattt -attatataattatatataattatataattatttattatataattatat------------ ------------ataattatataattatttattatataattatatataattatataattat -ttattatataattatatataattatataattatt-tattatataattatatataattata -taattatttattatataattatatataattatataattatttattatataattatatata -atatacaattatttattatataattatatataatatacaattatttattatataattata -tataattatatatttattatatttattatacagttatataataaa----tatataattat -atataaatatataattatatataattatatatatataattatatgtaattatatataatt -atataattattatataattgtatataatatataattatataattatatattatttattat -ataatatataattatataattatatattatttattatataatatataattatataattat -atattatttattatataattatatattatttattatatatattatttattatataattat -ataattatatattatttattatataattatatattatttattatataa-tatataattat -atattatttattatataa-tatataattatatattatttattatataattatatattatg -tattatataatatataattatatattatgtattatataattatataattatatattattt -attatataattatataattatatattatttattacataattatatattatttattacata -agtatatattatttattacataagtatatatcacttattatataattgtatataattatt -tattatataattgcatataattatttattatataattgtatatagttatttattatataa -ttctatatagttatatttattatacagttatataataaataattatataattatatataa -ttatatattatttattatctaattctatattaaatataattatttattatctaattctat -attatatataattatttattatataattctatattatatataattattatataatt ->p:HG002_2_chr20:8661834-8662229 -taacttcagtatttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacc -cagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatata -attatataattatttattatataattatatataattatataattatttattatataatta -tatataa-tatacaattatttattatataattatatataa-tatacaattatttattata -taattatatataattatatatttattatatttat-----tatacagttatataataaata -attatataattatatataattatat-atatataattatatataattatatataattatat -aattatatataattg-tatataattatttattatataattatatatta-tttattat--a -taattatataattatatat-----tatttattatatattatataatt------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------atataattatatattatttattatata-----atatataattatatat---- ----tatttattatataattatatattatttatta---------tatatattatttattat -ata----------------------attatatattatgtattatataattatataattat -atattatgtattatataat----------------tatatattatgtattatataattat -ataattatatattatgtattatataattatatattatttattatataattatataattat -atattatttattatataattatataattatatattatttattatataat----------- -----------tatataattatatattatttattatataattatataattatatattattt ---------attatataattatatattatttattatataattatatattatttattacata -aatatatattatttattacataagtatatatcacttattatataattgcatataattatt -tattatataattgcatataa----ttattatatatttat-----tatatttattatacag -t---------------------------tatataataaataattatataattatatataa -ttatatattatttattatctaattctatattaaatataattatttattatctaattctat -attatatataattatttattatataattctatattatatataattattatataatt ->ref_chr20:8661834-8662229 -taacttcagtatttaataaatcttcagtgaaaggcaagaggctacacacagtgacagacc -cagagataaaccctgtgcccctagagatttgcactcctcttaaaagtgtatatatatata -attatataattatttattatataattatatataattatat-------------------- --------------aattatttattatataattatatataa-tatacaattatttattata -taattatatataattatatatttattatatttat-----tatacagttatataataaata -attatataattatatataattatat-attatttattatctaattctat------------ ------------atta-aatataattatttattatctaattctatatta-tatataattat -ttattatataattctatat-----tatatataat-tattatataatt------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0d2e507e60453c89bd248c945dc7f54d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0d2e507e60453c89bd248c945dc7f54d.msa deleted file mode 100644 index 948c549e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0d2e507e60453c89bd248c945dc7f54d.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:32722324-32723312 -acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct -cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg -gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc -acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa -aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc -tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc -actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc -gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac -gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa -tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg -aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactgc -actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa -ta-------aataataataataataataaagacttgtgatcctctccctctccctctccc -tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc -tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct -gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggt ->syndip_2_chr20:32722324-32723312 -acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct -cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg -gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc -acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa -aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc -tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc -actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc -gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac -gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa -tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg -aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacaccactgc -actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa -taaataaataataataataataataataaagacttgtgatcctctccctctccctctccc -tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc -tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct -gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggt ->p:HG002_1_chr20:32722324-32723312 -acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct -cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg -gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc -acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa -aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc -tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc -actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc -gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac -gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa -tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg -aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacaccactgc -actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa -ta-------aataataataataataataaagacttgtgatcctctccctctccctctccc -tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc -tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct -gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggt ->p:HG002_2_chr20:32722324-32723312 -acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct -cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg -gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc -acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa -aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc -tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc -actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc -gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac -gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa -tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg -aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactgc -actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa -ta-------aataataataataataataaagacttgtgatcctctccctctccctctccc -tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc -tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct -gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggt ->ref_chr20:32722324-32723312 -acagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccct -cagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttctg -gccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagatc -acctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctactaa -aaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaaggc -tgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgcc -actgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggcc -gagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatcac -gaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaaa -tacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggctg -aggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactgc -actccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataaa -ta-------aataataataataataataaagacttgtgatcctctccctctccctctccc -tctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgtc -tccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgct -gccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgcc -tgcgattgcaggcacgcgccgccacgcctgactggt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0dd22c519e7416f2e879bd43c26d9682.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0dd22c519e7416f2e879bd43c26d9682.msa deleted file mode 100644 index 3d9e7894..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0dd22c519e7416f2e879bd43c26d9682.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:34235650-34236313 -agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca -ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga -gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag -gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat -gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga -aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag -aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa -ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa -aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa -agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag -gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcggg ->syndip_2_chr20:34235650-34236313 -agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca -ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga -gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag -gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat -gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga -aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag -aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa -ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa -aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa -agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag -gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcggg ->p:HG002_1_chr20:34235650-34236313 -agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca -ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga -gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag -gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat -gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga -aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag -aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa -ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa -aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa -agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag -gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcagg ->p:HG002_2_chr20:34235650-34236313 -agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca -ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga -gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaag -gaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaat -gaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagga -aggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaag -aaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaaa -ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaaa -aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa -agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag -gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcagg ->ref_chr20:34235650-34236313 -agcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccca -ggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacaga -gtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaggaaggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaag -gaaggaagga-------------------------------------------------- ------aaggaaggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagga -aggaaggaaggagggagggagggaaga--------------------------aggaaag -aaggaaggaaggagaaagagagaaagagagagagaagaagaaagagaaagaaacagaaaa -ggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaag--aa -aggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaaa -agaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctctag -gtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataat -cccagcactttgggaggccgaagcggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0e0f63391bc73f5d0919f9b9085bad03.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0e0f63391bc73f5d0919f9b9085bad03.msa deleted file mode 100644 index 4ef2d131..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0e0f63391bc73f5d0919f9b9085bad03.msa +++ /dev/null @@ -1,335 +0,0 @@ ->syndip_1_chr20:64173328-64176440 -aggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcct -agtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtg -tccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccattt -cccctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctcc -ctgacttctcctcctgcagcatctttccttgtagttgtgtccatttcccctccctggctt -ctcctcctgcagcatctttcc---tagttgtgtccatttcccctccctgacttctcctcc -tgcagcatccttccctgtagttgtgtccatttcccctccctgacttctcctcctgcagca -tctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttcc -ttgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagt -tgtg-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------tccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctt -tccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcctagttgt -gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat---- ------------------------------------------------------------- -------------------------------------ttcccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattccccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccc -tgacttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtc -tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctag -ttgtgtccattccccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggctcctgcagcatctttccctgtagttgtgtccattccccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -ttccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -ttccccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctcctgc -agcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttc -ctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattc -cccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccattccccctccctggcgt---ctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggctt---ctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtag -ttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgc ->syndip_2_chr20:64173328-64176440 -aggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcct -agtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtg -tccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccattt -cccctccctgacttctcctcctgcagcatctttcc------------------------- ------------------------------------------------------------- -------------------------tagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcag-- ----------------------------------------------------catctttcc -ttgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gtagcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctt -tcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgt -gtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gtagcatctttccctgtagttgtgtccattccccctccctgacttctcctgcagcatctt -tccctgtagttgtgtccat----------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------tccccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc--- -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccattt------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------cccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggctt--------------------------------- ------------------------ctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctcctgc -agcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttc -ctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattc -cccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccattccccctccctggctc---ctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggctt---ctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctgc-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------- ->p:HG002_1_chr20:64173328-64176440 -aggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcct -agtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtg -tccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccattt -cccctccctgacttctcctcctgcagcatctttcc------------------------- ------------------------------------------------------------- -------------------------tagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcag-- ----------------------------------------------------catctttcc -ttgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagt -tgtg-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------tccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctt -tccctgtagttgtgtccat----------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------ttcccctccctggcttctcctgca -gcatctttccctg----------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------tagttgtgtccatttcccctcc----------- ----------------------------------------ctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtag -ttgtgtccattc------------------------------------------------ -----------------------------------------------------cccctccc -tgacttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtc -tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctc------------------ ------------------------------------------------------------- --------------ctcctgcagcatctttccctgtagttgtgtccattccccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -ttccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggctt--------------------------------- ------------------------------------------------------------- --------------ctcctgtagcatctttccctgtagttgtgtccattccccctccctga -cttctc------------------------------------------------------ --------------------------------------------ctcctgcagcatctttc -ctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattc -cccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccattccccctccctggctc---ctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggctt---ctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctgc-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------- ->p:HG002_2_chr20:64173328-64176440 -aggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcct -agtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtg -tccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccattt -cccctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctcc -ctgacttctcctcctgcagcatctttcc---tagttgtgtccatttcccctccctgactt -ctcctcctgcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcc -tgcagcatctttccttgtagttgtgtccatttcccctccctgacttctcctcctgcagca -tctttccctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcc -ttgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagt -tgtgtccattccccctccctggcttctcctgtagcatctttccctgtagttgtgtccatt -tcccctccctggctt--------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------ctcctgcagcatccttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctt -tccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcctagttgt -gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttc -tcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctcct---------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------gtagcatctttcctagttgtgtccatttcccctcc----------- ----------------------------------------ctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccc -tgacttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtc -tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctag -ttgtgtccattccccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggctcctgcagcatctttccctgtagttgtgtccattccccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -ttccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -ttccccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctcctgc -agcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttc -ctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattc -cccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccattccccctccctggcgt---ctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggctt---ctcctgcagcatctttc -cctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtag -ttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgc ->ref_chr20:64173328-64176440 -aggtgcggctgatagagtgggtgtcttttgtgggcttctccccagcctgtggcctggcct -agtcagtagagatggtcaggggagcaggagggagcccataccccagtgcctgtagttgtg -tccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccattt -cccctccctgacttctcctcctgcagcatccttccctttagttgtgtccatttcccctcc -ctgacttctcctcctgcagcatctttcc-------------------------------- -------------------------tagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcag-- ----------------------------------------------------catctttcc -ttgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttccctgtagt -tgtg-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------tccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctt -tccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttcctagttgt -gtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat---- ------------------------------------------------------------- -------------------------------------ttcccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctcct---------------- ------------------------------------------------------------- ----------------------cctgcagcatctttccctgtagttgtgtccattccccct -ccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccc -tgacttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcgtc -tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgta -gcatctttcctagttgtgtccatttcccctccctggcttctc------------------ ------------------------------------------------------------- --------------ctcctgcagcatctttccctgtagttgtgtccattccccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -ttccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -ttccccctccctgacttctcctcctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctcctgc -agcatctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttc -ctagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattc -cccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttccctgtagttgtgtccattccccctccctggcgtctcctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttc -cctgtagttgtgtccattccccctccctggcttctcctcc-------------------- ----------------------------------tgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccct -ccctggcttctcctgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_0f3bae65383d9a283d74d67c5999b3cd.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_0f3bae65383d9a283d74d67c5999b3cd.msa deleted file mode 100644 index 805a1cd1..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_0f3bae65383d9a283d74d67c5999b3cd.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:57190146-57190538 -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -c----agagtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccag -agggggtgaggctggagagagtgagccaggaaccagaggaggtgaggccaga----gtga -gtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcac ->syndip_2_chr20:57190146-57190538 -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg -aaggggtgaggctggagacagtgagcgaggaacca------------------------- ------------gagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcac ->p:HG002_1_chr20:57190146-57190538 -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg -aaggggtgaggctggagacagtgagcgaggaacca------------------------- ------------gagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcac ->p:HG002_2_chr20:57190146-57190538 -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg -aaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtga -gtgaggagcccgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcac ->ref_chr20:57190146-57190538 -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg -aaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtga -gtgaggagcccgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_151cd5647644273b7c9d77245b35afe5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_151cd5647644273b7c9d77245b35afe5.msa deleted file mode 100644 index 66268bd9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_151cd5647644273b7c9d77245b35afe5.msa +++ /dev/null @@ -1,120 +0,0 @@ ->syndip_1_chr20:55627243-55628551 -tgtatcagctatccactacatacttagaaatttggctaattatcataacataaattaaca -ttttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactag -tatgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgt -tcatgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaat -ttatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtat -attacatatacataatacataaaatgtttaatacatacataatatatacataatataata -ttgtatattattaaattatacatgtatatatgtatactatatgtatatatgtatacaaaa -tatgtatataatatatacaaaaatatgtgtatttttgtacatatattgtacaaaaatatg -tatattatatatacaaaatatgtatataatatatacatatattatgtaatataatatata -cataatgtgtattacatacattatatgtaatatatacatatattatata---atatatat -gtatatattatatacatatatattatatacatatatgtatatattatata---------- --------catatatgtatacattatatattatgtatacatatatgtatatatgtatacat -tatatattatgtatacatatatgtatatatgtatacattatatattatgtatacatatat -gtatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatata -ttatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtatat -atgtatacattatatattatgtatacatatatgtata----------------------- ------------------------------------------------------------- ------------tatgtatacatgtatatacatatatacgtatacacatatatacgtg--- ------tatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgt -gtgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtat -acataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttt -agttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatca -tatttggttat ->syndip_2_chr20:55627243-55628551 -tgtatcagctatccactacatacttagaaatttggctaattatcataacataaattaaca -ttttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactag -tatgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgt -tcatgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaat -ttatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtat -attacatatacataatacataaaatgtttaatacatacataatatatacataatataata -ttgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaa -tatgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatg -tatattatatatacaaaatatgtatataatatatacatatattatgtaatataatatata -cgtaatgtgtattacatacattatatgtaatatatacatatatattatatacatatatat -gtatatattatatacatatatattatatacatatatgtatatattatatattatgtatac -acatatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatat -tatatattatgtatacac--------atatgtatatattatatattatgtatacacatat -gtatatatgtatatattatatattatgtatac--------acatatgtatatattatata -ttatgtatacacatatgtatatatgtatatattatatattatgtatacacatatgtatat ---------attatatattatgtatacacatatgtatatattatatat------------- ------------------------------------------------------------- ------------tatgtatacacgtatatacatatatacgtatacacgtatatacgta--t -atacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgt -gtgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtat -acataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttt -agttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatca -tatttggttat ->p:HG002_1_chr20:55627243-55628551 -tgtatcagctatccactacatacttagaaatttggctaattatcataacataaattaaca -ttttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactag -tatgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgt -tcatgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaat -ttatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtat -attacatatacataatacataaaatgtttaatacatacataatatatacataatataata -ttgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaa -tatgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatg -tatattatatatacaaaatatgtatataatatatacatatattatgtaatataatatata -cgtaatgtgtattacatacattatatgtaatatatacatatatattatatacatatatat -gtatatattatatacatatatattatatacatatatgtatatattatatattatgtatac -acatatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatat -tatatattatgtatacac--------atatgtatatattatatattatgtatacacatat -gtatatatgtatatattatatattatgtatac--------acatatgtatatattatata -ttatgtatacacatatgtatatatgtatatattatatattatgtatacacatatgtatat ---------attatatattatgtatacacatatgtatatattatatat------------- ------------------------------------------------------------- ------------tatgtatacacgtatatacatatatacgtatacacgtatatacgta--t -atacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgt -gtgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtat -acataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttt -agttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatca -tatttggttat ->p:HG002_2_chr20:55627243-55628551 -tgtatcagctatccactacatacttagaaatttggctaattatcataacataaattaaca -ttttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactag -tatgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgt -tcatgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaat -ttatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtat -attacatatacataatacataaaatgtttaatacatacataatatatacataatataata -ttgtatattattaaattatacatgtatatatgtatactatatgtatatatgtatacaaaa -tatgtatataatatatacaaaaatatgtgtatttttgtacatatattgtacaaaaatatg -tatattatatatacaaaatatgtatataatatatacatatattatgtaatataatatata -cataatgtgtattacatacattatatgtaatatatacatatattatata---atatatat -gtatatattatatacatatatattatatacatatatgtatatattatata---------- --------catatatgtatacattatatattatgtatacatatatgtatatatgtatacat -tatatattatgtatacatatatgtatatatgtatacattatatattatgtatacatatat -gtatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatata -ttatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtatat -atgtatacattatatattatgtatacatatatgtata----------------------- ------------------------------------------------------------- ------------tatgtatacatgtatatacatatatacgtatacacatatatacgtg--- ------tatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgt -gtgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtat -acataggagagagtcactgccctgagtcttaaatgtaacccttattaaagaaaatatttt -agttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatca -tatttggttat ->ref_chr20:55627243-55628551 -tgtatcagctatccactacatacttagaaatttggctaattatcataacataaattaaca -ttttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactag -tatgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgt -tcatgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaat -ttatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtat -attacatatacataatacataaaatgtttaatacatacataatatatacataatataata -ttgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaa -tatgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatg -tatattatatatacaaaatatgtatataatatatacatatattatgtaatataatatata -cataatgtgtattacatacattatatgtaatatatacatatatattatatacatatatat --tatata-catatatgtatatattatatacatatatgtatatattatatattatgtatac -acatatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatat -tatatattatgtatacacatatgtatatatgtatatattatatattatgtatacacatat -gtatatatgtatatattatatattatgtatacatatatgtatatatgtatatattatata -ttatgtatacatatatgtatatatgtatatattatatattatgtatacatatatgtatat ---------attatatattatgtatacatatatgtatatattatatattatgtatacatat -atgtatatattatatattatgtatacatatatgtatatattatatattatgtatacatat -atgtatatatgtatgtatacatgtatatacatatatacgtatacacatatatacgtgtat -atacatatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgt -gtgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtat -acataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttt -agttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatca -tatttggttat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_15a28d8e71c394df3beae7346f9310e2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_15a28d8e71c394df3beae7346f9310e2.msa deleted file mode 100644 index f58dc1df..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_15a28d8e71c394df3beae7346f9310e2.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:24681887-24682378 -actctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgcca -gttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcat -gcagcaggaggcaaactgtgaagtacctctctggc------------------------- ----------------------------------ctggcctttgtgaattaccacagtgc- ----------------------------------------------------------ggg -gtccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggt -ttacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtct -atgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacct -cagagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccg -aggaggagac ->syndip_2_chr20:24681887-24682378 -actctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgcca -gttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcat -gcagcaggaggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtc -aggggtctacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcag -gggtccacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcaggg -gtccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggt -ttacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtct -atgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacct -cagagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccg -aggaggagac ->p:HG002_1_chr20:24681887-24682378 -actctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgcca -gttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcat -gcagcaggaggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtc -aggggtccacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcag -gggtccacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcaggg -gtccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggt -ttacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtct -atgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacct -cagagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccg -aggaggagac ->p:HG002_2_chr20:24681887-24682378 -actctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgcca -gttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcat -gcagcaggaggcaaactgtgaagtacctctctggc------------------------- ----------------------------------ctggcctttgtgaattaccacagtgc- ----------------------------------------------------------ggg -gtccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggt -ttacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtct -atgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacct -cagagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctctg -aggaggagac ->ref_chr20:24681887-24682378 -actctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgcca -gttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcat -gcagcaggaggcaaactgtgaagtacctctctggc------------------------- ----------------------------------ctggcctttgtgaattaccacagtgcg -gggtccacccaggaaactgtgaagtacctctgtggcctttgtgaattaccacagtcaggg -gtccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggt -ttacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtct -atgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacct -cagagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccg -aggaggagac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_1a3fa27fa27f5a48ddc2961cb2908c18.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1a3fa27fa27f5a48ddc2961cb2908c18.msa deleted file mode 100644 index 85ac9a87..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_1a3fa27fa27f5a48ddc2961cb2908c18.msa +++ /dev/null @@ -1,370 +0,0 @@ ->syndip_1_chr20:63167363-63167674 -ctaatacttaccaaattaattccagatttggagtcactcatggttcccaccagcactcag -ccccatctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagcc -ccctcctcagcccccacctccgcccccacctcagcccctcctcagcccccacctcagccc -cctcctcagcccccacctccgcccccacctccgcccccacctctgcccctcctcagcccc -cacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc -t-------------------------------------------------cctcagcccc -cacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc -t-------------cctcagcccccacctcagccccctcctcag---------------- -------------------------------cccccacctccgccccctcctcagccccca -cctctgcccct------------cctcagcccccacctcagccccctcctcagcccccac -ctccgcccccacctccgcccccacctccgcccctcctccgcccccacctcagcccccacc -tcc-----------------------gccccctcctcagcccccacctctgcccctcctc -agcccccacctcagcccccacctcagcccccacctc------------------------ ------------------------------------------------------------- -------------ccccctcctcagcccccacctcagcccccacctcagccccctcctcag -cccccacctcagcccccacctccgcccct------------cctcagcccccacctccgc -ccccacctcagcccccacctcagcccccacctccgcccccacctcagcccccacctccgc -ccccacctcagcccccacctccgcccccacctcagcccccacctctgcccctcctcagcc -cccacctccgccccctcctcagcccccacctctg-------------------------- -----------cccctcctcagcccccacctcagcccccacctcagcccccacctcc-ccc -ctcctcagcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccc -cacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccct -cctcagcccccacctcag------------------------------------------ -----------------------------------------------------ccccctcc -tcagcccccacctccgcccccacctccgcccccacctctgcccctcctcagcccccacct -cagccccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctc -cgcccccacctcagcccccacctccgccccct---------------------------- -------cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctcagc -ccccacct-------------------------cccccctcctcagcccccacctcagcc -cccacctccgcccctcctcagcccccacctccgccccca--------------------- ---------------------------------------cctcagcccccacctcagcccc -cacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc----- -------gcccccacctcagcccccacctctgcccctcctcagcccccacctccgccccct -cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctcagcccccac -ct-------------------------cccccctcctcagccccca-------------- ----------------------cctcagcccccacctcagccccctcctcagcccccacct -cagcccccacctcagcccccacctccgcccctcctcagccccca---------------- --------cctcagcccccacctccgcccctcctccgcccccacctcagccccctcctcag -cccccacctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagc -cccctcctcagcccccacctc-------------------------------------cc -ccctcctccgcccccacctcagcccccacctcagcccccacctcagcccccacctc---- ------------------------------------------------------------- --------------------------------------------ccccctcctccgccccc -acctcagccccca-----------cctcagcccccacctccgcccccacctcagccccca -cctcc------------------------------------------------------- ----------------------------------------------------cccctcctc -agcccccacctcagcccccacctccgccccca-----------cctcagcccccacctca -gcccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcag -cccccacctcagcccccacctccgccccca------------------------------ ----------------------------------------cctcagcccccacctccgccc -ccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctccgccc -ccacctcc-----------gcccccacctcagcccccacctcagcccccacctccgcccc -ca----------------------------------------------cctcagccccca -cctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccctcc -tcagcccccacctcagcccccacctcagcccccacctcagcccct--------------- -----------cctcagcccccacctcagccccctcctcagccccctcctcagcccccacc -tcagcccccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctc -agcccccacctcagccc------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------cctcagcccccacctcagcccccacctc -cgcccccacctccgcccccacctcc----------------------------------- -------------------------------------------------gcccctcctcag -cccccacctcagcccccacctcagcccctcctcagcccccacctcc-------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------accccc -acctccgtccccacctccgccccctcctcagccccctcctcagcccccacctcagccccc -acctccgcccccacctcagcccctcctcagcccccacctccgcccccacctcagaccctc -ctcagcccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccc -tcaggagttggcaccccacaggctccttcccttcccacctccgccacaccctgacg ->syndip_2_chr20:63167363-63167674 -ctaatacttaccaaattaattccagatttggagtcactcatggttcccaccagcactcag -ccccatctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagcc -ccctcctcagcccccacctccgcccccacctccgccccctcctcagcccctcctccgccc -ccacctcagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccc -cacctcagcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccc -cacctcagccccctcctcagcccccacctcagcccccacctccgcccccacctcagcccc -cacctcagccccctcctcagcccccacctcagcccccacctcagcccccacctcagcccc -ctcctcagcccccacctcagcccccacctccgccccctcctcagcccccacctccccccc -acctccgccccctcctcagcccccacctcccccccacctccgccccctcctcagccccca -cctctgcccctcctcaggccccacctcagcccccacctcagccccctcctcagcccccac -ctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacc -tccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcccctcctc -agcccccacctcagcccccacctccgcccccacctcagcccccacctcagcccccacctc -cccccctcctcagcccccacctccacccccacctcagcccccacctcagcccccacctcc -ccccctcctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcag -cccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgc -ccccacctccgcccccacctcagcccccacctccgccccctcctcagcccccacctcagc -ccccacctcagcccccacctccacccccacctcagcccccacctcagcccccacctcccc -cccacctccgccccctcctcagcccccacctctgcccctcctcaggccccacctcagccc -ccacctcagccccctcctcagcccccacctcagcccccacctcagcccccacctccgccc -ctcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgcccc -cacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccct -cctctgcccccacctcagccccctcctcagcccccacctctgcccctcctcagcccccac -ctcagcccccacctccgcccccacctcagcccccacctcagcccccacctccccccctcc -tcagcccccacctccacccccacctcagcccccacctccgcccctcctcagcccccacct -cagcccccacctccacccccacctcagcccccacctccgcccccacctccgcccctcctc -agcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcag -cccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccac -ccccacctcagcccccacctcagcccccacctcccccccacctccgccccctcctcagcc -cccacctctgcccctcctcaggccccacctcagcccccacctcagccccctcctcagccc -ccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccc -cacctccacccccacctcagcccccacctccgcccccacctcagcccccacctccgcccc -tcctcagcccccacctcagcccccacctccgcccctcctctgcccccacctcagccccct -cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctccgcccccac -ctcagcccccacctcagcccccacctccccccctcctcagcccccacctccacccccacc -tcagcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacct -cagcccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacctc -agcccctcctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcag -ccccctcctccgcccctcctcagcccccacctccacccccacctcagcccccacctcagc -cccctcctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcagcc -cccacctccgccccctcctcagcccccacctcagcccccacctcagccccctcctccacc -cctcctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccc -cacctccacccccacctcagcccccacctccgcccctcctcagcccccacctccgccccc -acctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagccccca -cctccgcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcc -tcagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctc -agcccccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctcc -gcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcca -cccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctccgc -ccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccacctccgccc -ccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcagccc -ccacctccgcccctcctcagcccccacctcagcccccacctcagaccccacctccgcccc -cacctccgcccctcctcagcccccacctcagcccccacctcagcccctcctcagccccca -cctccgcccccacctccgcccccacctccgcccctcctcagcccccacctcagcccctcc -tcagcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacc -tccgcccccacctcagccccctcctcagcccccacctcagccccctcctcagcccccacc -tcagcccccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctc -agcccccacctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcag -ccccctcagcccccacctcagcccccacctccgcccccacctccgcccctcctcagcccc -cacctcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgccccc -acctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagccccca -cctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcccccacc -tcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccccacctc -cgcccccacctccgcccccacctccgcccccacctcagcccctcctcagcccccacctca -gcccccacctcagccccctcctcagcccccacctccgcccccacctcagcccctcctcag -cccccacctcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgc -ccccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagcc -cccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcccc -cacctcagcccctcctcagccccctcctcagcccccacctcagcccccacctcagccccc -acctccgcccccacctccgcccccacctcagccccctcctcagccccctcctcagccccc -acctccgcccccacctcagcccctcctcagcccccacctccgcccccacctcaga----- -------ccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccc -tcaggagttggcaccccacaggctccttcccttcccacctccgccacaccctgacg ->p:HG002_1_chr20:63167363-63167674 -ctaatacttaccaaattaattccagatttggagtcactcatggttcccaccagcactcag -ccccatctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagcc -ccctcctcagcccccacctccgcccccacctccgccccctcctcagcccctcctccgccc -ccacctcagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccc -cacctcagcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccc -cacctcagccccctcctcagcccccacctcagcccccacctccgcccccacctcagcccc -cacctcagccccctcctcagcccccacctcagcccccacctcagcccccacctcagcccc -ctcctcagcccccacctcagcccccacctccgccccctcctcagcccccacctccccccc -acctccgccccctcctcagcccccacctcccccccacctccgccccctcctcagccccca -cctctgcccctcctcaggccccacctcagcccccacctcagccccctcctcagcccccac -ctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacc -tccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcccctcctc -agcccccacctcagcccccacctccgcccccacctcagcccccacctcagcccccacctc -cccccctcctcagcccccacctccacccccacctcagcccccacctcagcccccacctcc -ccccctcctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcag -cccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgc -ccccacctccgcccccacctcagcccccacctccgccccctcctcagcccccacctcagc -ccccacctcagcccccacctccacccccacctcagcccccacctcagcccccacctcccc -cccacctccgccccctcctcagcccccacctctgcccctcctcaggccccacctcagccc -ccacctcagccccctcctcagcccccacctcagcccccacctcagcccccacctccgccc -ctcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgcccc -cacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccct -cctctgcccccacctcagccccctcctcagcccccacctctgcccctcctcagcccccac -ctcagcccccacctccgcccccacctcagcccccacctcagcccccacctccccccctcc -tcagcccccacctccacccccacctcagcccccacctccgcccctcctcagcccccacct -cagcccccacctccacccccacctcagcccccacctccgcccccacctccgcccctcctc -agcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcag -cccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccac -ccccacctcagcccccacctcagcccccacctcccccccacctccgccccctcctcagcc -cccacctctgcccctcctcaggccccacctcagcccccacctcagccccctcctcagccc -ccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccc -cacctccacccccacctcagcccccacctccgcccccacctcagcccccacctccgcccc -tcctcagcccccacctcagcccccacctccgcccctcctctgcccccacctcagccccct -cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctccgcccccac -ctcagcccccacctcagcccccacctccccccctcctcagcccccacctccacccccacc -tcagcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacct -cagcccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacctc -agcccctcctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcag -ccccctcctccgcccctcctcagcccccacctccacccccacctcagcccccacctcagc -cccctcctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcagcc -cccacctccgccccctcctcagcccccacctcagcccccacctcagccccctcctccacc -cctcctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccc -cacctccacccccacctcagcccccacctccgcccctcctcagcccccacctccgccccc -acctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagccccca -cctccgcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcc -tcagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctc -agcccccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctcc -gcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcca -cccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctccgc -ccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccacctccgccc -ccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcagccc -ccacctccgcccctcctcagcccccacctcagcccccacctcagaccccacctccgcccc -cacctccgcccctcctcagcccccacctcagcccccacctcagcccctcctcagccccca -cctccgcccccacctccgcccccacctccgcccctcctcagcccccacctcagcccctcc -tcagcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacc -tccgcccccacctcagccccctcctcagcccccacctcagccccctcctcagcccccacc -tcagcccccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctc -agcccccacctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcag -ccccctcagcccccacctcagcccccacctccgcccccacctccgcccctcctcagcccc -cacctcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgccccc -acctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagccccca -cctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcccccacc -tcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccccacctc -cgcccccacctccgcccccacctccgcccccacctcagcccctcctcagcccccacctca -gcccccacctcagccccctcctcagcccccacctccgcccccacctcagcccctcctcag -cccccacctcagcccccacctcagcccctcctcagcccccacctccgcccccacctccgc -ccccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagcc -cccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctcagcccc -cacctcagcccctcctcagccccctcctcagcccccacctcagcccccacctcagccccc -acctccgcccccacctccgcccccacctcagccccctcctcagccccctcctcagccccc -acctccgcccccacctcagcccctcctcagcccccacctccgcccccacctcaga----- -------ccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccc -tcaggagttggcaccccacaggctccttcccttcccacctccgccacaccctgacg ->p:HG002_2_chr20:63167363-63167674 -ctaatacttaccaaattaattccagatttggagtcactcatggttcccaccagcactcag -ccccatctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagcc -ccctcctcagcccccacctcagcccccacctccgcccccacctcagcccctcctcagccc -ccacctccgcccccacctccgcccccacctccgcccccacctctgcccctcctcagcccc -cacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc -t-------------------------------------------------cctcagcccc -cacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc -t-------------cctcagcccccacctcagccccctcctcag---------------- -------------------------------cccccacctccgccccctcctcagccccca -cctctgcccct------------cctcagcccccacctcagccccctcctcagcccccac -ctccgcccccacctccgcccccacctccgcccctcctccgcccccacctcagcccccacc -tcc-----------------------gccccctcctcagcccccacctctgcccctcctc -agcccccacctcagcccccacctcagcccccacctc------------------------ ------------------------------------------------------------- -------------ccccctcctcagcccccacctcagcccccacctcagccccctcctcag -cccccacctcagcccccacctccgcccct------------cctcagcccccacctccgc -ccccacctcagcccccacctcagcccccacctccgcccccacctcagcccccacctccgc -ccccacctcagcccccacctccgcccccacctcagcccccacctctgcccctcctcagcc -cccacctccgccccctcctcagcccccacctctg-------------------------- -----------cccctcctcagcccccacctcagcccccacctcagcccccacctcc-ccc -ctcctcagcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccc -cacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccct -cctcagcccccacctcag------------------------------------------ -----------------------------------------------------ccccctcc -tcagcccccacctccgcccccacctccgcccccacctctgcccctcctcagcccccacct -cagccccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctc -cgcccccacctcagcccccacctccgccccct---------------------------- -------cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctcagc -ccccacct-------------------------cccccctcctcagcccccacctcagcc -cccacctccgcccctcctcagcccccacctccgccccca--------------------- ---------------------------------------cctcagcccccacctcagcccc -cacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc----- -------gcccccacctcagcccccacctctgcccctcctcagcccccacctccgccccct -cctcagcccccacctctgcccctcctcagcccccacctcagcccccacctcagcccccac -ct-------------------------cccccctcctcagccccca-------------- ----------------------cctcagcccccacctcagccccctcctcagcccccacct -cagcccccacctcagcccccacctccgcccctcctcagccccca---------------- --------cctcagcccccacctccgcccctcctccgcccccacctcagccccctcctcag -cccccacctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagc -cccctcctcagcccccacctc-------------------------------------cc -ccctcctccgcccccacctcagcccccacctcagcccccacctcagcccccacctc---- ------------------------------------------------------------- --------------------------------------------ccccctcctccgccccc -acctcagccccca-----------cctcagcccccacctccgcccccacctcagccccca -cctcc------------------------------------------------------- ----------------------------------------------------cccctcctc -agcccccacctcagcccccacctccgccccca-----------cctcagcccccacctca -gcccccacctcagcccccacctccgcccctcctcagcccccacctccgcccccacctcag -cccccacctcagcccccacctccgccccca------------------------------ ----------------------------------------cctcagcccccacctccgccc -ccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctccgccc -ccacctcc-----------gcccccacctcagcccccacctcagcccccacctccgcccc -ca----------------------------------------------cctcagccccca -cctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccctcc -tcagcccccacctcagcccccacctcagcccccacctcagcccct--------------- -----------cctcagcccccacctcagccccctcctcagccccctcctcagcccccacc -tcagcccccacctccgcccccacctccgcccccacctcagccccacctcagcccctcctc -agcccccacctcagccc------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------cctcagcccccacctcagcccccacctc -cgcccccacctccgcccccacctcc----------------------------------- -------------------------------------------------gcccctcctcag -cccccacctcagcccccacctcagcccctcctcagcccccacctcc-------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------accccc -acctccgtccccacctccgccccctcctcagccccctcctcagcccccacctcagccccc -acctccgcccccacctcagcccctcctcagcccccacctctgcccccacctcagaccctc -ctcagaccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccc -tcaggagttggcaccccacaggctccttcccttcccacctccgccacaccctgacg ->ref_chr20:63167363-63167674 -ctaatacttaccaaattaattccagatttggagtcactcatggttcccaccagcactcag -ccccatctcagcccccatctcagcccccaccgcagcctcacctcagtgcccacctcagcc -ccctcctcagccccca-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------cctcagccccc -acctccgcccccacctcagcccctcctcagcccccacctccgcccccacctcaga----- -------ccctcctcagcccctcctcatcccctcctcagcagctgctggaatgggctaccc -tcaggagttggcaccccacaggctccttcccttcccacctccgccacaccctgacg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_1d20ababbd3c82b9d4be9155373214aa.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1d20ababbd3c82b9d4be9155373214aa.msa deleted file mode 100644 index a0be7d9f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_1d20ababbd3c82b9d4be9155373214aa.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:23560783-23561291 -taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat -tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca -gcattcctttctctctctttctttctttctttctttctttccttccttccttccttcctt -ccttccttccttccttccttccttccttcct----------------------------- ------------------------------------------------------------- -----------------------ttctttctttctttctttctttctttctttctttcttt -ttttctttct-------ttctttctttctttttcttttacagagtcttactcttgttgcc -caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctggga ->syndip_2_chr20:23560783-23561291 -taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat -tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca -gcattcctttctctctctttctttctttctttctttctttctttctttctttctttcttt -ctttctttccttccttccttccttccttccttccttccttccttccttccttctttcctt -ctttccttctttccttctttccttctttccttctttccttctttccttctttccttcttt -ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt -ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc -caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctggga ->p:HG002_1_chr20:23560783-23561291 -taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat -tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca -gcattcctttctctctctttctttctttctttctttctttctttctttctttctttcttt -ctttctttccttccttccttccttccttccttccttccttccttccttccttctttcctt -ctttccttctttccttctttccttctttccttctttccttctttccttctttccttcttt -ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt -ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc -caggctgtagtgcagtggtgtgatctcggctgactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctggga ->p:HG002_2_chr20:23560783-23561291 -taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat -tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca -gcattcctttctctctctttctttctttctttctttctttccttccttccttccttcctt -ccttccttccttccttccttccttccttcct----------------------------- ------------------------------------------------------------- -----------------------ttctttctttctttctttctttctttctttctttcttt -ttttctttct-------ttctttctttctttttcttttacagagtcttactcttgttgcc -caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctggga ->ref_chr20:23560783-23561291 -taaaatcttcatacagaagatataagagatttgcaaattaccgttatagtattagagtat -tctgaatgtcagtatgtacttagtttcactagggagatttttattccctaatgttcttca -gcattcctttctctttctttctttctttctttctttctttctttctttctttctttcctt -ctttccttccttccttccttccttccttccttccttccttccttccttccttccttcctt -ctttccttctttccttctttccttctttccttctttccttctttccttctttcc------ -------ttctttccttctttccttctttctttctttctttctttctttctttctttcttt -ctttctttctttctttcttctttctttctttttcttttacagagtcttactcttgttgcc -caggctgtagtgcagtggtgtgatctcggctcactgcaacctccacctctgcctcctgca -ttcaagaaattctcctgcctcagcctccagagtagctggga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_1fde3de72e50bf9b46fe45bb9ee1204f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_1fde3de72e50bf9b46fe45bb9ee1204f.msa deleted file mode 100644 index 6fd35d8c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_1fde3de72e50bf9b46fe45bb9ee1204f.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:63964695-63966223 -ggtgtccaggctgtccgcagccctgcagggagcaggtgaggtgagggccaggagggccta -actgtgggccccattacccccaggccgtggccgaggagcaccctgacctggaacgagccc -ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttctcacc -actgttcctccccgacctgggacgagcccccataccttttctcaccactgt---tccccg -acctgggacgagcccccataccttttcttaccactgttcctccctgtggcacgaggtgct -----------------ttgttctccgacctggtcagcagcaccat--------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------tttgcagggcggtgt ->syndip_2_chr20:63964695-63966223 -ggtgtccaggctgtccgcagccctgcagggagcaggtgaggtgagggccaggagggccta -actgtgggccccattacccccaggccgtggccgaggagcaccctgacctggaacgagccc -ccataccttttctcaccactgttccccgacctgggacaagcccccataccttttcttacc -actgt---tccctgacctgggacgagcccccataccttttctcaccactgt---tccctg -acctgggacgagcccccataccttttctcaccactgttccccgacctgggacgagccccc -ataccttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccac -tgttcctccccgacctgggacgagcccccataccttttctcaccactgttccccgacctg -ggacgagcccccataccttttctcaccactgttccctgacctggaacgagcccccatacc -ttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttc -cccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggacgagc -ccccataccttttctcaccactgttccccgacctgggacgagcccccataccttttctca -ccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctgacct -gggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccatac -cttttcttaccactgttccccgacctgggacgagcccccataccttttcttaccactgtt -cctccccgacctgggacgagcccccataccttttctcaccactgttcctccccaacctgg -gacgagcccccataccttttctcaccactgttcctccccgacctgggacgagcccccata -ccttttctcaccactgttccctgacctgggacgagcccccataccttttcttaccactgt -tcctccccgacctgggacgagcccccataccttttcttaccactgttcctccccgacctg -ggacgagcccccataccttttcttaccactgttcctccccgacctgggacgagcccccat -accttttcttaccactgttccccgacctgggacgagcccccataccttttctcaccactg -ttccctgacctgggacgagcccccataccttttcttaccactgttccctgacctgggacg -agcccccataccttttctcaccactgttcctccccgacctgggacgagcccccatacctt -ttctcaccactgttccccgacctgggacgagcccccataccttttcttaccactgttcct -ccctgacctgggacgagcccccataccttttcttaccactgttcctccccgacctgggac -gagcccccataccttttcttaccactgttcctccctgtggcacgaggtgctttgttctcc -gacctggtcagcagcaccattttgcagggcggtgt ->p:HG002_1_chr20:63964695-63966223 -ggtgtccaggctgtccgcagccctgcagggagcaggtgaggtgagggccaggagggccta -actgtgggccccattacccccaggccgtggccgaggagcaccctgacctggaacgagccc -ccataccttttctcaccactgttccccgacctgggacaagcccccataccttttcttacc -actgt---tccctgacctgggacgagcccccataccttttctcaccactgt---tccctg -acctgggacgagcccccataccttttctcaccactgttccccgacctgggacgagccccc -ataccttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccac -tgttcctccccgacctgggacgagcccccataccttttctcaccactgttccccgacctg -ggacgagcccccataccttttctcaccactgttccctgacctggaacgagcccccatacc -ttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttc -cccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggacgagc -ccccataccttttctcaccactgttccccgacctgggacgagcccccataccttttctca -ccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctgacct -gggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccatac -cttttcttaccactgttccccgacctgggacgagcccccataccttttcttaccactgtt -cctccccgacctgggacgagcccccataccttttctcaccactgttcctccccaacctgg -gacgagcccccataccttttctcaccactgttcctccccgacctgggacgagcccccata -ccttttctcaccactgttccctgacctgggacgagcccccataccttttcttaccactgt -tcctccccgacctgggacgagcccccataccttttcttaccactgttcctccccgacctg -ggacgagcccccataccttttcttaccactgttcctccccgacctgggacgagcccccat -accttttcttaccactgttccccgacctgggacgagcccccataccttttctcaccactg -ttccctgacctgggacgagcccccataccttttcttaccactgttccctgacctgggacg -agcccccataccttttctcaccactgttcctccccgacctgggacgagcccccatacctt -ttctcaccactgttccccgacctgggacgagcccccataccttttcttaccactgttcct -ccctgacctgggacgagcccccataccttttcttaccactgttcctccccgacctgggac -gagcccccataccttttcttaccactgttcctccctgtggcacgaggtgctttgttctcc -gacctggtcagcagcaccattttgcagggcggtgt ->p:HG002_2_chr20:63964695-63966223 -ggtgtccaggctgtccgcagccctgcagggagcaggtgaggtgagggccaggagggccta -actgtgggccccattacccccaggccgtggccgaggagcaccctgacctggaacgagccc -ccataccttttctcaccactgttccccgacctgggacgagcccccataccttttcttacc -actgttcctccctgacctgggacgagcccccataccttttcttaccactgttcctccccg -acctgggacgagcccccataccttttcttaccactgttcctccctgtggcacgaggtgct -----------------ttgttctccgacctggtcagcagcaccat--------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------tttgcagggcggtgt ->ref_chr20:63964695-63966223 -ggtgtccaggctgtccgcagccctgcagggagcaggtgaggtgagggccaggagggccta -actgtgggccccattacccccaggccgtggccgaggagcaccctgacctggaacgagccc -ccataccttttctcaccactgttccccgacctgggacaagcccccataccttttcttacc -actgt---tccctgacctgggacgagcccccataccttttctcaccactgt---tccctg -acctgggacgagcccccataccttttctcaccactgttccccgacctgggacgagccccc -ataccttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccac -tgttcctccccgacctgggacgagcccccataccttttctcaccactgttccccgacctg -ggacgagcccccataccttttctcaccactgttccctgacctggaacgagcccccatacc -ttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttc -cccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggacgagc -ccccataccttttctcaccactgttccccgacctgggacgagcccccataccttttctca -ccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctgacct -gggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccatac -cttttcttaccactgttccccgacctgggacgagcccccataccttttcttaccactgtt -cctccccgacctgggacgagcccccataccttttctcaccactgttcctccccaacctgg -gacgagcccccataccttttctcaccactgttcctccccgacctgggacgagcccccata -ccttttctcaccactgttccctgacctgggacgagcccccataccttttcttaccactgt -tcctccccgacctgggacgagcccccataccttttcttaccactgttcctccccgacctg -ggacgagcccccataccttttcttaccactgttcctccccgacctgggacgagcccccat -accttttcttaccactgttccccgacctgggacgagcccccataccttttctcaccactg -ttccctgacctgggacgagcccccataccttttcttaccactgttccctgacctgggacg -agcccccataccttttctcaccactgttcctccccgacctgggacgagcccccatacctt -ttctcaccactgttccccgacctgggacgagcccccataccttttcttaccactgttcct -ccctgacctgggacgagcccccataccttttcttaccactgttcctccccgacctgggac -gagcccccataccttttcttaccactgttcctccctgtggcacgaggtgctttgttctcc -gacctggtcagcagcaccattttgcagggcggtgt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_20bd20e862e124e808d69a4270d4895a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_20bd20e862e124e808d69a4270d4895a.msa deleted file mode 100644 index 3b13513e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_20bd20e862e124e808d69a4270d4895a.msa +++ /dev/null @@ -1,110 +0,0 @@ ->syndip_1_chr20:5041757-5042809 -cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt -gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta -gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat -gcataac------------------------------ttttttttttttttttttttgag -acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg -tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg -cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg -ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca -acatttgtaaacccttggttcattgtgcttctccctttattactc--------------- --ttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg -cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc -ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------ttctttttcttttttgtatttttagtagagatgg -ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca -gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt -ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt -gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga -cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccat ->syndip_2_chr20:5041757-5042809 -cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt -gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta -gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat -gcgtaacttttttttttttttttttttttttttttttttttttttttttttttttttgag -acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg -tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg -cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg -ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca -acatttgtaaacccttggttcattgtgcttctccctttattactcttttttttttttttt -tttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg -cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc -ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------ttctttttcttttttgtatttttagtagagatgg -ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca -gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt -ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt -gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga -cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccat ->p:HG002_1_chr20:5041757-5042809 -cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt -gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta -gcgggatttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat -gcgtaacttttttttttttttttttttttttttttttttttttttttttttttttttgag -acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg -tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg -cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg -ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca -acatttgtaaacccttggttcattgtgcttctccctttattactcttttttttttttttt -tttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg -cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc -ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------ttctttttcttttttgtatttttagtagagatgg -ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca -gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt -ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt -gatctgctcgtcttggcctcccaaagtgttgggattataggcatgagccaccacaaccga -cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccat ->p:HG002_2_chr20:5041757-5042809 -cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt -gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta -gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat -gcataac------------------------------ttttttttttttttttttttgag -acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcaccgcaacctg -tgcctcccaggttcaagtgatctcctgcctcagcctccccagtacctaggattacaggtg -cgcgcctccagcatagctaatgtttgtatttttagtagaaacggggtttcaccatgttgg -ccaggatggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca -acatttgtaaacccttggttcattgtgcttctccctttattactc--------------- --ttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg -agcactctcggttcactgcaacctccacctcataggttcaagcgattctcctgcctcagc -ctcctgagtagctgggattacaggtgcccaccaccatgcccagctaatttttttttttga -gagtctcacactgtcgcccaggctggagtgcaatggcactatcttgactcactgcaacct -cctcctgtgttcacgtgattctcctgcctcagcctcctgagtagctgggattacaggcac -atgccaccatgcccggctaatttttctttttttttttttttgtatttttagtagagatgg -ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccgcctcg -gactcccaaagtgctgggattacaggtgtgagccaccgtgcccggcctaattttgtattt -ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcccgatctcaggt -gatccgctcgtcttggcctcccaaagtgttgggattacaggcatgagccaccacacccag -cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccat ->ref_chr20:5041757-5042809 -cagtgttggagcctgcagatgctgacagtgcctgcagctttcctgcctattttaggactt -gctagaagcttggcatgtcctaaaaaccctttttcaagagtctctccccagctgctgcta -gcggga-ttttttttttaactctctatcctatttaacctcctcactgatgaccttttaat -gcgtaac----------------------------ttttttttttttttttttttttgag -acggagtctcgctctcccaggctggagtgcagtggtgtgatctcggctcactgcaacctg -tgcctcccaggttcaagcgatctcctgcctcagcctccccagtacctaggattacaggtg -cgcgcctccagcatagctaatgtttgtatttttagtagagacggggtttcaccatgttgg -ccaggctggttatgcataactttttatcacagatgtttgatctcagttttaatcttttca -acatttgtaaacccttggttcattgtgcttctccctttattactc----ttttttttttt -tttttttttttttttttgagacggagtttcgctcttgttgcccaggctggagtgcagtgg -cgcactctcggttcactgcaatctccacctcataggttcaagcgattctcctgcctcagc -ctcctgagtagctgggattacaggcacacgccaccatgcctggctaattt---------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------ttctttttcttttttgtatttttagtagagatgg -ggtttcactatgttggccagactggtcttgaactcctgacctcgtgatctgcccacctca -gactcccaaagtgctgggattacaggtgtgagccaccgtgcctggcctaattttgtattt -ttagtagagacggggtttctccatgttggtcaggctggtctcgaactcctgacctcaggt -gatctgctcgtcttggcctcccaaagtgttgggattataggcataagccaccacaaccga -cctgactgctcatttttaaactcttgatctgacactgggggactttaagctataatcttg -ttctgttttttttctttttctcttgccttctatgctttccat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_21a50aece69afd2b8a6bc9496f1128d8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_21a50aece69afd2b8a6bc9496f1128d8.msa deleted file mode 100644 index fd295d79..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_21a50aece69afd2b8a6bc9496f1128d8.msa +++ /dev/null @@ -1,410 +0,0 @@ ->syndip_1_chr20:64131803-64133966 -gcctcccctgtcccagacttctcctggcctctctcatgtcctatgagaccccctcactgt -ccaccctcatgtcctgtagagaccccctcactgtccactctcatggcctatagagacccc -ctcactgtcaactctcatgtcctatg-agaccccctcactgtccactctcatggcctgta -gagaccccctcactgtccaccctcatgt-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------cctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtccta -t-gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatag -agaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatg -tcctgtagagaccccctcactgtccaccctcatgtcctat-------------------- ------------------------------------------------------------- ---------------------------------------------------------gaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactct -catgtcctat-gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccactctcatgtcctatgagaccccctcactgtccactctcatg -gcctgtagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagaga -ccccctcactgtccactctcatgtcctatagagaccccctcactgtccaccctcatggcc -tatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccactc -tcatggcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcact -gtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggccta -t-gagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccctc -atgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcgtgtcctata---------------------------------gagaccccct -cactgtccaccctcatgtcctatagagaccccctcactgtccgccctcatgtcctat-ga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtccaccctcgtgtcctat--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------agagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccgccctcatgtccta-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------tgagaccccctcact -gtccaccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatgtcctatg-------------------------------- ------------------------------------agaccccctcactgtccaccctcat -gtcctatgagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctatagagaccccctc -actgtccaccctcgtgtcctat-gagaccccctcactgtccaccctcatgtcctatagag -accccctcactgtcca----------------------------------ccctcatgtc -ctat-gagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccact -ctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcact -gtcaactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagac- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------cccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtcaactctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc-aaa -gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtcc -accctcatgtcc-aaagagaccccctcactgtccaccctcatggcctgtagagaccccct -cactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctataga -gaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccctcatggc -ctg--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------tagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccactctcatgtcctatgagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatgagac -cccctcactgtccaccctcatgtcctatgagaccccctcactgtccacccatatggcctg -tagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagacccc -ctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctct -gcatttgctccttgggttcccggaacttgagc ->syndip_2_chr20:64131803-64133966 -gcctcccctgtcccagacttctcctggcctctctcatgtcctatgagaccccctcactgt -ccaccctcatgtcctgtagagaccccctcactgtccactctcatggcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagacccctcactgtccaccctcatg -g----------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------cctat-gagacc -ccctcactgtccactctcatgtcctatagagaccccctcactgtccaccctcgtgtccta -tagagaccccctcactgtccaccctcatgtcctatagaga-cccctcactgtccaccctc -atggcctat-gagaccccctcactgtccaccctcatggcctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatag -agaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatg -tcctgtagagaccccctcactgtccaccctcatgtcctat-------------------- ------------------------------------------------------------- ---------------------------------------------------------gaga -ccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccct -catgtcctatagagaccccctcactgtccactctcatgtcctatagagaccccctcactg -tccaccctcatggcctatagagaccccctcactgtccaccctcatggcctgtagagaccc -cctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatggcctat -a--------------------------------gagaccccctcactgtccaccctcatg -gcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcca -ccctcatggcctgtagagaccccctcactgtccaccctcatggcctat-gagaccccctc -actgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagaga -ccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccgccctcatgtcctat-gagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtccta -t-gagaccccctcactgtccaccctcatgtcctatgaga--cccctcactgtccaccctc -atgtcctatgagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtc -cactctcatgtcctat----------------------------------gagaccccct -cactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctataga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtcaactctcatgtcctat--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------gagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgtccaa-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------agagaccccctcact -gtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagacc -ccctcactgtccaccctcatggcctata-------------------------------- -----------------------------------gagaccccctcactgtccaccctcat -gtccaaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcca -ccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatagag -accccctcactgtcca----------------------------------ccctcgtgtc -ctatagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagac- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------cccctcactgtccaccctcgtgtcctatagagaccccctcactgt -ccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatagagacccc -ctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatggcctata -gagaccccctcactgtccaccctcat-gtccaaagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccacccatatggcctgtagagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccct -cactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtaga -gaccccctcactgtccaccctcatggcctatgagaccccctcactgtccaccctcatggc -ctg--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------tagagaccccctcactgtccaccctcatgtccta -tagagacccctcactgtccaccctcatgtcctata------------------------- ------------------------------------------gagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagac -cccctcactgtccaccctcatgtccta--------------------------------- -tagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccacccatatggcctgtagagacccc -ctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctct -gcatttgctccttgggttcccggaacttgagc ->p:HG002_1_chr20:64131803-64133966 -gcctcccctgtcccagacttctcctggcctctctcatgtcctatgagaccccctcactgt -ccaccctcatgtcctgtagagaccccctcactgtccactctcatggcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagacccctcactgtccaccctcatg -gcctatgagaccccctcactgtccactctcatgtcctatagagaccccctcactgtccac -cctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagacccctcac -tgtccaccctcatggcctatgagaccccctcactgtccaccctcatggcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtccta -t-gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatag -agaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccactctcatgtcctatagagaccccctcactgtcca -ccctcatggcctatgagaccccctcactgtccactctcatggcctatagagaccccctca -ctgtccaccctcatggcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtccaccct -catgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactg -tccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccgccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctat -a--------------------------------gagaccccctcactgtccaccctcatg -gcctgtagagaccccctcactgtccgccctcatgtcctat-gagaccccctcactgtcca -ccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctat-gaga -ccccctcactgtccaccctcatgtcctatgaga--cccctcactgtccaccctcatgtcc -tat-gagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactc -tcatgtcctatgaga--------------------------------------------- --------------------------cccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtcaactctcatgtccta -t-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atgtccaaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -caccctcatggcctgta---------------------------------gagaccccct -cactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcc------ ------------------------------aaagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtccaccctcatggcctgt--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------agagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgtccaa-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------agagaccccctcact -gtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgtagagacc -ccctcactgtccaccctcatgtcctata-------------------------------- ------------------------------------------------------------- ------------------------------------------gagaccccctcactgtcca -ccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctc -actgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagag -accccctcactgtcca----------------------------------ccctcatgtc -ctatagagaccccctcactgtccaccctcgtgtcctat---------------------- ------------agagaccccctcactgtccaccctcgtgtcctatagagaccccctcact -gtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatagagac- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------cccctcactgtccaccctcgtgtcctatagagaccccctcactgt -ccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc---- ------------------------------------------------------------- ---------------------------------------tatagagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcatggcctataga -gaccccctcactgtccaccctcatggcctatgagaccccctcactgtccaccctcatggc -ctg--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------tagagaccccctcactgtccaccctcatgtccta -tagagacccctcactgtccaccctcatgtcctata------------------------- ------------------------------------------gagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagac -cccctcactgtccaccctcatgtccta--------------------------------- -tagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcgtggcctgtagagaccccctcactgtccaccctcatggcctgtagagacccc -ctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctct -gcatttgctccttgggttcccggaacttgagc ->p:HG002_2_chr20:64131803-64133966 -gcctcccctgtcccagacttctcctggcctctctcatgtcctatgagaccccctcactgt -ccaccctcatgtcctgtagagaccccctcactgtccactctcatggcctatagagacccc -ctcactgtccaccctcatggcctgta---------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccaccctcatgtcctat-gagaccccctcactgtccaccctcgtgtcctatagagacc -ccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctc -atgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-ga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccact -ctcatgtcctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagacc -ccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccactctcatgtcctatgagaccccctcactgtccactctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtcc -accctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcctatagag -accccctcactgtccaccctcatggcctatgagaccccctcactgtccactctcatggcc -tatagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccc -tcatggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcact -gtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctatagagacc -ccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatgtcctat -gagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccctcat -gtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccgccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagag -accccctcactgtccaccctcatggcctgtagagaccccctcactgtccgccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcact -gtccaccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccaccctcatgtcctatgagacccctcactgtccaccctcatgt -cctatgagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactc -tcatgtcctatgagacccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtcaactctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc-aaa -gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtcc -accctcatgtcc-aaagagaccccctcactgtccaccctcatggcctgtagagaccccct -cactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctataga -gaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccctcatggc -ctgtagagaccccctcactgtccacccatatggcctgtagagaccccctcactgtccacc -ctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcac -tgtccaccctcatggcctatagagaccccctcactgtccactctcatgtcctatgagacc -ccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtccta -tgagaccccctcactgtccactctcatgtcctatgagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatgagac -cccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatggccta -tagagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagacccc -ctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctct -gcatttgctccttgggttcccggaacttgagc ->ref_chr20:64131803-64133966 -gcctcccctgtcccagacttctcctggcctctctcatgtcctatgagaccccctcactgt -ccaccctcatgtcctgtagagaccccctcactgtccactctcatggcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgt-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------cctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtccta -t-gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatgagaccccc -tcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatag -agaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccactctcatgtcctatagagaccccctcactgtcca -ccctcatggcctatgagaccccctcactgtccactctcatggcctatagagaccccctca -ctgtccaccctcatggcctatagagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtccaccct -catgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactg -tccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccgccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctat -a--------------------------------gagaccccctcactgtccaccctcatg -gcctgtagagaccccctcactgtccgccctcatgtcctat-gagaccccctcactgtcca -ccctcatgtcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctc -actgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctat-gaga -ccccctcactgtccaccctcatgtcctatgaga--cccctcactgtccaccctcatgtcc -tat-gagaccccctcactgtccaccctcatgtcctat-gagaccccctcactgtccactc -tcatgtcctatgaga--------------------------------------------- --------------------------cccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtcaactctcatgtccta -t-gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctc -atgtccaaagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtc -caccctcatggcctgta---------------------------------gagaccccct -cactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcc------ ------------------------------aaagagaccccctcactgtccaccctcatgg -cctgtagagaccccctcactgtccaccctcatggcctgt--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------agagaccccctcactgtccaccctcatgtcctatagagaccccct -cactgtccaccctcatgtccaa-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------agagaccccctcact -gtccaccctcatggcctgtagagaccccctcactgtccacccatatggcctgtagagacc -ccctcactgtccaccctcatgtcctata-------------------------------- ------------------------------------------------------------- ------------------------------------------gagaccccctcactgtcca -ccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctc -actgtccaccctca---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------tggcctgtagagaccccctcactgtccaccctcatggcctgtagagacccc -ctcactgtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctct -gcatttgctccttgggttcccggaacttgagc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2374d8355030cbadee4ced684237da5f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2374d8355030cbadee4ced684237da5f.msa deleted file mode 100644 index fe1ec416..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2374d8355030cbadee4ced684237da5f.msa +++ /dev/null @@ -1,660 +0,0 @@ ->syndip_1_chr20:63693224-63693985 -atcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactg -gtaaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagag -tcctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccc -tatgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacctt -caccaccaccacctccaccaccacctccaccacctccacctccaccacctccaccacctc -caccaccaccacctccaccaccaccacctccaccaccaccaccaccaccacctccaccac -caccaccaccaccaccacctccacctccaccacctccaccaccacctccacctccaccac -cacctccacctccacctccaccaccaccacctccaccacctccaccacctccacctccac -caccacctccacctccaccaccacctccacctccacctccacctccacctccaccaccac -cacctccaccacctccaccacctccacctccaccaccaccacctccacctccacctccac -cacctccacctccaccacctccacctccaccacctccaccaccaccaccaccaccaccac -cacctccaccaccaccaccaccaccacctccaccacctccacctccaccacctccaccac -caccacctccaccaccacctccaccaccacctccacctccaccacctccacctccaccac -ctccacctccacctccaccaccacctccaccacctccaccaccacctccaccacctccac -ctccaccaccaccacctccaccaccaccaccaccaccacctccaccacctccacctccac -cacctccaccaccaccacctccaccaccacctccaccaccacctccacctccaccacctc -cacctccaccacctccacctccacctccaccaccacctccaccacctccaccaccacctc -caccacctccaccacctccaccaccacctccaccacctccacctccaccaccaccacctc -cacctccaccaccaccacctccaccaccacctccacctccaccaccaccacctccacctc -caccaccaccacctccaccaccacctccaccaccaccaccaccaccaccacctccacctc -caccacctccaccaccaccaccaccacctccacctccaccacctccaccacctccaccac -caccaccaccacctccaccacctccaccaccacctccaccacctccacctccaccaccac -cacctccaccaccaccacctccacctccacctccacctccacctccaccaccacctccac -ctccaccaccacctccaccaccacctccacctccaccacctccacctccacctccaccac -ctccaccaccaccaccaccaccaccaccaccaccaccacctccaccacctccacctccac -ctccaccaccaccaccaccacctccaccaccaccaccaccacctccaccacctccaccac -cacctccaccaccaccaccaccaccaccaccaccacctccaccacctccacctccacctc -cacctccaccacctccaccacctccaccaccacctccaccaccaccaccaccacctccac -caccacctccacctccaccaccacctccaccaccacctccacctccaccacctccacctc -caccacctccaccacctccacctccaccacctccacctccacctccaccacctccaccac -caccaccaccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctc -caccacctccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccacctc -caccaccacctccacctccaccaccacctccaccaccacctccacctccaccacctccac -ctccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctccacctc -caccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctccaccac -ctccaccaccacctccacctccaccacctccaccaccacctccaccaccacctccaccac -caccacctccaccaccacctccaccacctccaccaccacctccacctccaccacctccac -caccacctccaccaccacctccaccaccaccacctccaccaccacctccaccacctccac -caccacctccacctccaccacctccacctccacctccaccacctccaccaccaccaccac -caccaccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctc -cacctccaccacctccaccaccacctccacctccaccacctccacctccacctccaccac -ctccacctccaccacctccacctccacctccaccacctccaccaccaccacctccaccac -cacctccaccacctccaccaccacctccacctccaccacctccaccaccacctccaccac -cacctccaccaccaccacctccaccaccacctccaccacctccaccaccacctccacctc -caccacctccacctccacctccaccacctccaccaccaccaccaccaccaccaccaccac -caccacctccaccaccaccacctccaccaccacctccaccaccaccaccaccacctccac -caccaccaccaccacctccaccaccacctccaccacctccaccaccaccaccaccaccac -caccacctccaccaccacctccaccaccaccaccaccaccaccaccacctccaccacctc -cacctccaccaccaccaccacctccaccaccaccaccaccaccacctccacctccaccac -caccacctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccac -caccaccacctccaccacctccaccacctccaccaccacctccaccacctccaccaccac -caccaccacctccaccaccacctccaccaccaccaccaccaccaccacctccacctccac -ctccaccacctccacctccaccacctccacctccaccacctccacctccacctccaccac -ctccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccaccac -ctccaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacctc -caccaccaccacctccaccacctccaccaccacctccaccacctccacctccaccaccac -cacctccaccaccaccacctccacctccaccaccaccaccaccaccacctccacctccac -caccacctccaccaccacctccacctccacctccaccacctccaccaccacctccaccac -ctccaccacctccacctccaccaccaccaccacctccaccaccaccaccaccacctctac -cacctctaccaccaccaccaccacctccaccaccaccaccaccacctccaccaccaccac -caccaccacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccac -ctccacctccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccac -cacctccaccaccaccaccacctccaccaccacctccaccaccacctccaccacctccac -caccaccaccacctccacctccaccacctccaccaccacctccaccaccaccaccaccac -cacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctccac -ctccaccaccaccaccacctccacctccaccaccaccaccaccaccaccaccaccaccac -ctccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccac -cacctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccaccac -cacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccaccaccac -ctccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccacctccac -cacctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccaccac -cacctccaccaccaccaccaccaccaccacctccaccaccacctccaccaccacctccac -cacctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccaccac -cacctccaccaccacctccaccaccaccaccaccaccacctccaccaccacctccaccac -ctccaccaccaccaccaccacctctaccacctctaccaccaccaccaccacctccaccac -caccaccacctccaccaccaccaccacctccaccaccaccacctccacctccaccaccac -cacctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccaccac -ctccaccacctccaccaccaccaccaccaccaccaccacctccaccaccaccaccaccac -cacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctctac -caccaccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccaccac -cacctccaccaccaccacctccacctccaccaccaccacctccaccaccaccacctccac -ctccaccaccaccacctccaccacctccaccaccacctccaccaccaccacctccacctc 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------------------------ccaccaccacctccacctccaccaccacctccaccac -cacctccaccaccaccacct---------------ccacctccaccaccaccacctccac -ctccaccaccaccaccaccaccacctccaccaccacctccacctccacca---ccacctc -cacctccaccacctccaccaccagcaccaccaccacctccaccaccaccacctccacctc -caccaccaccaccaccaccacct---------------------ccaccaccacctccac -ctccacctccacctccaccaccacctccaccaccacctccacca---------------- ------------------------------------------------------------- ---------------------------------------------------cctccaccac -cacctccacctccaccacctccacctccacctccaccacctccacctccacctccaccac -ctccacct---------------------------------------------------- ---------------ccacctccacctccaccaccaccacct------------------- ---------------------------------ccacctccacctccacctccaccacgtc -caccacctccaccacctccacctccacctccacctccacctccaccacct---------- ---------------------------------ccacctccacctccaccacctccacctc -cacctccacctccaccacgtccaccaccaccacctccaccaccaccaccaccacctcca- ---------------------ccaccacctccacctccaccaccacctccaccaccacctc 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-caccacctccacctccacctccaccacctccaccaccacctccaccacctccaccaccac -ctccacct---------------------------------------------------- ---------ccaccacctccaccaccacctccaccacctccaccacctccaccaccaccac -caccacct---------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------ccaccacctccaccaccacctccaccacctccacctccacctccac -ct---------------------------------ccacctccaccaccacctccaccac -ctccaccaccacctccacctccaccacctccacctccacctccaccacctccaccaccac -cacctccaccaccacctccaccaccaccacctccacctccaccaccacctccaccacctc ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------caccacctccaccaccacctccaccac -ctccaccacctccaccaccaccacc---------------------------------ac -cacctccaccacctccaccaccacctccaccaccaccacctccacctccacctccaccac 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---------------------------------ccacctccacctccaccacctccacctc -cacctccacctccaccacgtccaccaccaccacctccaccaccaccaccaccacctcca- ---------------------ccaccacctccacctccaccaccacctccaccaccacctc -caccaccaccacctccacctccaccaccaccacctccacctccaccaccaccaccaccac -ca---------------------------------------------------------- ---------------------------------------------------------cctc -caccaccacctccacctccaccaccacctccacctccaccacctccaccaccaccaccac -ctccacctccacca------------------ccaccacctccacctccacctccacctc -caccaccacctccaccaccacctccaccaccaccacctccacctccacca---------- ---ccaccaccaccaccacctccaccaccacctccacctccaccaccacctccaccaccac -ctccaccacctccaccaccaccaccacctccacctccaccaccaccacctccacctccac -caccaccaccaccaccacctccaccaccacctccacctccaccaccacctccaccacctc -cacctccacctccacctccacctccaccacctccacctccacctccaccaccaccaccac -ctccaccacct------------------------------------------------- ---ccaccaccacctccaccacctccacctccacctccacctccaccaccacctccaccac -ctccaccacca---------------------------------cctccaccacctccac 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-ctccaccacctccaccaccacctcca---------------------------------- ------------------------------------ccaccacctccaccaccacctcctc -cacctccaccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttg -ttggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgaccccta -agcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtc -aactgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctctgt -ttggggtggagtccaagtctc ->p:HG002_2_chr20:63693224-63693985 -atcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactg -gtaaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagag -tcctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccc -tatgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacctt -caccaccaccacctccaccaccacctccaccacctccacctccaccacctccaccacctc -caccaccaccacctccaccaccaccacctccaccaccaccaccaccaccacctccaccac -caccaccaccaccaccacctccacctccaccacctccaccaccacctccacctccaccac -cacctccacctccacctccaccaccaccacctccaccacctccaccacctccacctccac -caccacctccacctccaccaccacctccacctccacctccacctccacctccaccaccac 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-ctccaccaccaccaccaccacctccaccaccaccaccaccacctccaccacctccaccac -cacctccaccaccaccaccaccaccaccaccaccacctccaccacctccacctccacctc -cacctccaccacctccaccacctccaccaccacctccaccaccaccaccaccacctccac -caccacctccacctccaccaccacctccaccaccacctccacctccaccacctccacctc -caccacctccaccacctccacctccaccacctccacctccacctccaccacctccaccac -caccaccaccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctc -caccacctccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccacctc -caccaccacctccacctccaccaccacctccaccaccacctccacctccaccacctccac -ctccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctccacctc -caccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctccaccac -ctccaccaccacctccacctccaccacctccaccaccacctccaccaccacctccaccac -caccacctccaccaccacctccaccacctccaccaccacctccacctccaccacctccac -caccacctccaccaccacctccaccaccaccacctccaccaccacctccaccacctccac -caccacctccacctccaccacctccacctccacctccaccacctccaccaccaccaccac -caccaccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctc -cacctccaccacctccaccaccacctccacctccaccacctccacctccacctccaccac -ctccacctccaccacctccacctccacctccaccacctccaccaccaccacctccaccac -cacctccaccacctccaccaccacctccacctccaccacctccaccaccacctccaccac -cacctccaccaccaccacctccaccaccacctccaccacctccaccaccacctccacctc -caccacctccacctccacctccaccacctccaccaccaccaccaccaccaccaccaccac -caccacctccaccaccaccacctccaccaccacctccaccaccaccaccaccacctccac -caccaccaccaccacctccaccaccacctccaccacctccaccaccaccaccaccaccac -caccacctccaccaccacctccaccaccaccaccaccaccaccaccacctccaccacctc -cacctccaccaccaccaccacctccaccaccaccaccaccaccacctccacctccaccac -caccacctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccac -caccaccacctccaccacctccaccacctccaccaccacctccaccacctccaccaccac -caccaccacctccaccaccacctccaccaccaccaccaccaccaccacctccacctccac -ctccaccacctccacctccaccacctccacctccaccacctccacctccacctccaccac -ctccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccaccac -ctccaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacctc -caccaccaccacctccaccacctccaccaccacctccaccacctccacctccaccaccac -cacctccaccaccaccacctccacctccaccaccaccaccaccaccacctccacctccac -caccacctccaccaccacctccacctccacctccaccacctccaccaccacctccaccac -ctccaccacctccacctccaccaccaccaccacctccaccaccaccaccaccacctctac -cacctctaccaccaccaccaccacctccaccaccaccaccaccacctccaccaccaccac -caccaccacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccac -ctccacctccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccac -cacctccaccaccaccaccacctccaccaccacctccaccaccacctccaccacctccac -caccaccaccacctccacctccaccacctccaccaccacctccaccaccaccaccaccac -cacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctccac -ctccaccaccaccaccacctccacctccaccaccaccaccaccaccaccaccaccaccac -ctccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccac -cacctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccaccac -cacctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccaccaccac -ctccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccacctccac -cacctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccaccac -cacctccaccaccaccaccaccaccaccacctccaccaccacctccaccaccacctccac -cacctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccaccac -cacctccaccaccacctccaccaccaccaccaccaccacctccaccaccacctccaccac -ctccaccaccaccaccaccacctctaccacctctaccaccaccaccaccacctccaccac -caccaccacctccaccaccaccaccacctccaccaccaccacctccacctccaccaccac -cacctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccaccac -ctccaccacctccaccaccaccaccaccaccaccaccacctccaccaccaccaccaccac -cacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctctac -caccaccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccaccac -cacctccaccaccaccacctccacctccaccaccaccacctccaccaccaccacctccac -ctccaccaccaccacctccaccacctccaccaccacctccaccaccaccacctccacctc -caccaccaccacctccaccacctccaccaccaccacctccaccaccaccacctccaccac -ctccaccaccaccaccaccacctccaccacctccaccacctccaccaccaccaccaccac -ctccacctccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccac -caccacctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccac -caccaccaccacctccacctccacctccaccacctccaccaccaccacctccaccaccac -cacctccacctccaccacctccaccaccacctccaccaccaccacctccacctccaccac -caccacctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccac -cacctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccac -cacctccaccaccaccacctccaccacctccaccaccaccaccaccacctccaccacctc -caccacctccaccaccaccaccaccacctccacctccacctccaccacctccaccaccac -cacctccaccaccaccaccaccaccacctccaccacctccaccaccaccaccaccacctc -cacctccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccac -caccacctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccac -ctccaccaccacctccacctccacctccaccacctccacctccaccaccaccaccaccac -caccaccaccaccaccacctccacctccacctccaccaccaccacctctaccaccacctc -caccaccaccaccaccaccaccaccaccacctccaccacctccaccaccaccacctccac -caccaccacctccacctccaccaccaccaccacctccaccacctccaccaccacctccac -ctccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccacctc -caccacctccaccaccaccacctccaccaccaccacctccacctccaccacctccaccac -ctccaccaccaccaccacctccaccaccaccaccaccaccacctccacctccaccacctc -taccaccacctccaccaccaccaccaccaccacctccacctccaccacctccacctccac -cacctctaccaccacctccaccaccaccacctccacctccacctccaccaccaccacctc -cacctccacctccaccaccaccaccaccaccaccacctccaccaccaccaccaccaccac -caccaccacctccacctccaccaccaccacctccaccaccaccacctccaccacctccac -caccacctccacctccaccaccaccacctccacctccacctccaccaccaccaccaccac -ctccaccaccaccacctccaccaccaacacctccacctccacctccaccaccaccaccac -cacctccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacctc -caccaccacctccaccacctccaccaccaccacctccaccaccacctccaccaccaccac -caccaccacctccacctccacctccaccaccaccacctctaccaccacctccaccaccac -caccaccaccaccaccaccacctccacctccacctccaccacctccacctccaccaccac -caccaccaccaccacctccaccaccacctccacctccacctccaccacctccacctccac -caccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccaccaccac -ctctaccaccacctccaccaccaccaccaccaccaccaccaccacctccaccaccaccac -ctccacctccaccaccaccacctccacctccaccaccaccacctccacctccaccaccac -caccaccaccaccacctccaccaccaccacctccaccacctccaccaccacctccaccac -caccacctccaccacctccaccaccacctccacctccaccaccaccacctccaccaccac -cacctccacctccaccaccaccacctccacctccacctccaccacctccacctccaccac -ctccaccaccaccacctccaccacctccaccaccacctccacctccaccaccaccacctc -caccaccaccacctccaccacctccaccaccacctccacctccaccaccaccacctccac -ctccacctccaccaccaccaccaccacctccactaccaccacctccacctccaccaccac -cacctccaccaccaacacctccacctccacctccacctccaccaccaccacctccacctc -caccaccaccacctccaccaccaccacctccaccacctccacctccaccaccaccacctc -caccaccacctccaccaccaccaccacctccaccaccaccacctccaccaccacctccac -caccaccacctccaccaccacctccaccaccacctccacctccaccaccaccacctgcac -caccacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttg -ttggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgaccccta -agcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtc -aactgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctctgt -ttggggtggagtccaagtctc ->ref_chr20:63693224-63693985 -atcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactg -gtaaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagag -tcctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccc -tatgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacct------- ------------------------------------------------------------- ------------------------------------------------------------- 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------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------ccacctccacctccac -ct------------------------------------------------------ccac -ctccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccaccac -caccaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacct- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- 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------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------ccaccaccac -cacctccacctccaccaccacctccaccaccaccacctccacctccacca---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------ccacctccac -caccaccaccaccaccaccaccaccaccacca---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------ccacctccaccaccaccacctgcac -caccacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttg -ttggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgaccccta -agcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtc -aactgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctctgt -ttggggtggagtccaagtctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_239890d58a86aba7cea2e6af3b3cad8c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_239890d58a86aba7cea2e6af3b3cad8c.msa deleted file mode 100644 index e8d7de04..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_239890d58a86aba7cea2e6af3b3cad8c.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:20320229-20320629 -tgaggtgattggaaatttgaaacctggagagttaatgatgataagcaattatgattaatt -tttttagcagtaaagatggtatttcagatatatagatatatatatattatatatatgtaa -tatatataatatatgtaatatatattatatatatgtaatatatataatatatgtaatata -ttatatatatgtaatatatataatatatgtaatatatattatatatgtaatatatataat -atatgtaatatatattatatatgtaatata----atatatgtaatatatattatatatgt -aatatataatatatgtaatatatattatatatgtaatataatatatgtaatatatattat -atatgtaatatatattacatatattatatatgcaatatatattatatatattatatatgc -aatatatattatatatattatatatgcaatatatattatatatgcaatatatattatata -tattatatatgcaatatatattatatatattacatatgtaatatatattacatatgtaat -atataatatattatatattacatatgtaatatataatatattatatattacatatgtaat -atataatatatattacatatgtaatatataatatatattacatatgtaatatattatata -ttacatatgtaatatattatatattacatatgtaatatattatatattacatatgtaata -tattatatattacatatgtaatatattatatattacatatgtaatatatataatatatta -catatgtaatatataatatattatatatgtaatatatattacatatataatatatataat -atatatgtaatatattatatatattatatatgtaatatatattacatatataatatatat -tatatatattacatatattatatatgtaatatatattacatatgtaatatatgtaatata -tattacatatgtaatatatattatatatgtaatatatattacatatattatatatgtaat -atatattatatatattatatatgtaatgtataatatatatattatatatgtaatatatat -tatatataatatatgtaatatatattatatatgtaatgtatattatatatattatatatg -taatgtatattatatataatatatgtaatgtatattatatatgtaatatatattatgtat -attatatatgtaatatatattatatatattatatatgtaatatatattatatatattata -tatgtaatatatattatatatattatatatgtaatatatattatatatattatatatgta -atatatattatatatattatatatgtaatatatattatatatattatatatgtaatatat -attatatatattatatatgtaatatatattatatatattatatatgtaatatatattata -tatattatatatgtaatatatattatatatattatatatgtaatatatattatatatatt -atatatgtaatatatattatatatattatatatgtaatatatattatatatattatatat -gtaatatatattatatatattatatatgtaatatatatatatttaaaaacagaaccatta -tcttttagagatacatactgaagtgtctggagacatgcttcaagataacccaggagggag -aa ->syndip_2_chr20:20320229-20320629 -tgaggtgattggaaatttgaaacctggagagttaatgatgataagcaattatgattaatt -tttttagcagtaaagatggtatttcagatatatagatatatatatattatatatatgtaa -tatatataatatatgtaatatata---------------------------ttatatata -tgtaatatatataatatatgtaatatatgtaatatatattatatatgta----atataat -atatgtaatatatattatatatgtaatatata--------------------atatatgt -aatatataatatatgtaatatatattatatatgtaatata-------taatatatattat -atatgtaatatatatatatttaaaaacagaaccattatcttttagagatac--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------atactgaagtgtctggagacatgcttcaagataacccaggagggag -aa ->p:HG002_1_chr20:20320229-20320629 -tgaggtgattggaaatttgaaacctggagagttaatgatgataagcaattatgattaatt -tttttagcagtaaagatggtatttcagatatatagatatatatatattatatatatgtaa -tatatataatatatgtaatatata---------------------------ttatatata -tgtaatatatataatatatgtaatatatgtaatatatattatatatgta----atataat -atatgtaatatatattatatatgtaatatata--------------------atatatgt -aatatataatatatgtaatatatattatatatgtaatata-------taatatatattat -atatgtaatatatatatatttaaaaacagaaccattatcttttagagatac--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------atactgaagtgtctggagacatgcttcaagataacccaggagggag -aa ->p:HG002_2_chr20:20320229-20320629 -tgaggtgattggaaatttgaaacctggagagttaatgatgataagcaattatgattaatt -tttttagcagtaaagatggtatttcagatatatagatatatatatat--tatatatgtaa -tatatataatatatgtaatatgta--atatatataatatatgtaatatatattatatata -tgtaatatatataatatatgtaatatatgtaatatatattatatatgta----atataat -atatgtaatatatattatatatgtaatatataatatatgtaatatatatattatatatgt -aatatataatatatgtaatatatattatatatgtaatataatatatgtaatatatattat -atatgtaatatatattacatatattatatatgcaatatatattatatatattatatatgc -aatatatattatatatattatatatgcaatatatattatatatgcaatatatattatata -tattatatatgcaatatatattatatatattacatatgtaatatatattacatatgtaat -atataatatattatatattacatatgtaatatataatatattatatattacatatgtaat -atataatatatattacatatgtaatatataatatatattacatatgtaatatattatata -ttacatatgtaatatattatatattacatatgtaatatattatatattacatatgtaata -tattatatattacatatgtaatatattatatattacatatgtaatatatataatatatta -catatgtaatatataatatattatatatgtaatatatattacatatataatatatataat -atatatgtaatatattatatatattatatatgtaatatatattacatatataatatatat -tatatatattacatatattatatatgtaatatatattacatatgtaatatatgtaatata -tattacatatgtaatatatattatatatgtaatatatattacatatattatatatgtaat -atatattatatatattatatatgtaatgtataatatatatattatatatgtaatatatat -tatatataatatatgtaatatatattatatatgtaatgtatattatatatattatatatg -taatgtatattatatataatatatgtaatgtatattatatatgtaatatatattatgtat -attatatatgtaatatatattatatatattatatatgtaatatatattatatatattata -tatgtaatatatattatatatattatatatgtaatatatattatatatattatatatgta -atatatattatatatattatatatgtaatatatattatatatattatatatgtaatatat -attatatatattatatatgtaatatatattatatatattatatatgtaatatatattata -tatattatatatgtaatatatattatatatattatatatgtaatatatattatatatatt -atatatgtaatatatattatatatattatatatgtaatatatatgtaatatatattatat -atgtaatatataatatatattatatatgtaatatatatatatttaaaaacagaaccatta -tcttttagagatacatactgaagtgtctggagacatgcttcaagataacccaggagggag -aa ->ref_chr20:20320229-20320629 -tgaggtgattggaaatttgaaacctggagagttaatgatgataagcaattatgattaatt -tttttagcagtaaagatggtatttcagatatatagatatatatatattatatatatgtaa -tatatataatatatgtaatatata---------------------------ttatatata -tgtaatatatataatatatgtaatatatgtaatatatattatatatgta----atataat -atatgtaatatatattatatatgtaatatata--------------------atatatgt -aatatataatatatgtaatatatattatatatgtaatata-------taatatatattat -atatgtaatatatatatatttaaaaacagaaccattatcttttagagatac--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------atactgaagtgtctggagacatgcttcaagataacccaggagggag -aa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_24fd8ff0eec7e23320c9f4385933e3f5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_24fd8ff0eec7e23320c9f4385933e3f5.msa deleted file mode 100644 index b3b44011..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_24fd8ff0eec7e23320c9f4385933e3f5.msa +++ /dev/null @@ -1,120 +0,0 @@ ->syndip_1_chr20:55627244-55628550 -gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat -tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt -atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt -catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt -tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata -ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat -tgtatattattaaattatacatgtatatatgtatactatatgtatatatgtatacaaaat -atgtatataatatatacaaaaatatgtgtatttttgtacatatattgtacaaaaatatgt -atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac -ataatgtgtattacatacattatatgtaatatatacatatattatata---atatatatg -tatatattatatacatatatattatatacatatatgtatatattatata----------- -------catatatgtatacattatatattatgtatacatatatgtatatatgtatacatt -atatattatgtatacatatatgtatatatgtatacattatatattatgtatacatatatg -tatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatatat -tatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtatata -tgtatacattatatattatgtatacatatatgtata------------------------ ------------------------------------------------------------- -----------tatgtatacatgtatatacatatatacgtatacacatatatacgtg---- -----tatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg -tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata -cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta -gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggtta ->syndip_2_chr20:55627244-55628550 -gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat -tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt -atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt -catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt -tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata -ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat -tgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaat -atgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatgt -atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac -gtaatgtgtattacatacattatatgtaatatatacatatatattatatacatatatatg -tatatattatatacatatatattatatacatatatgtatatattatatattatgtataca -catatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatatt -atatattatgtatacac--------atatgtatatattatatattatgtatacacatatg -tatatatgtatatattatatattatgtatac--------acatatgtatatattatatat -tatgtatacacatatgtatatatgtatatattatatattatgtatacacatatgtatat- --------attatatattatgtatacacatatgtatatattatatat-------------- ------------------------------------------------------------- -----------tatgtatacacgtatatacatatatacgtatacacgtatatacgta--ta -tacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg -tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata -cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta -gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggtta ->p:HG002_1_chr20:55627244-55628550 -gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat -tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt -atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt -catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt -tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata -ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat -tgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaat -atgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatgt -atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac -gtaatgtgtattacatacattatatgtaatatatacatatatattatatacatatatatg -tatatattatatacatatatattatatacatatatgtatatattatatattatgtataca -catatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatatt -atatattatgtatacac--------atatgtatatattatatattatgtatacacatatg -tatatatgtatatattatatattatgtatac--------acatatgtatatattatatat -tatgtatacacatatgtatatatgtatatattatatattatgtatacacatatgtatat- --------attatatattatgtatacacatatgtatatattatatat-------------- ------------------------------------------------------------- -----------tatgtatacacgtatatacatatatacgtatacacgtatatacgta--ta -tacgtatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg -tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata -cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta -gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggtta ->p:HG002_2_chr20:55627244-55628550 -gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat -tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt -atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt -catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt -tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata -ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat -tgtatattattaaattatacatgtatatatgtatactatatgtatatatgtatacaaaat -atgtatataatatatacaaaaatatgtgtatttttgtacatatattgtacaaaaatatgt -atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac -ataatgtgtattacatacattatatgtaatatatacatatattatata---atatatatg -tatatattatatacatatatattatatacatatatgtatatattatata----------- -------catatatgtatacattatatattatgtatacatatatgtatatatgtatacatt -atatattatgtatacatatatgtatatatgtatacattatatattatgtatacatatatg -tatatatgtatacattatatattatgtatacatatatgtatatatgtatacattatatat -tatgtatacatatatgtatatatgtatacattatatattatgtatacatatatgtatata -tgtatacattatatattatgtatacatatatgtata------------------------ ------------------------------------------------------------- -----------tatgtatacatgtatatacatatatacgtatacacatatatacgtg---- -----tatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg -tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata -cataggagagagtcactgccctgagtcttaaatgtaacccttattaaagaaaatatttta -gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggtta ->ref_chr20:55627244-55628550 -gtatcagctatccactacatacttagaaatttggctaattatcataacataaattaacat -tttatggctgtgaaaagagaatagaaatggattttagaatgtcaagtatttatcactagt -atgtgttaatataaatagcttaataaaaatagggcatttatatgtatatatgtgggtgtt -catgtatatatttttatatgtatatatgtgggtgtgcatgtatacattaaatgatgaatt -tatatgtatatattaaatgtatatattatatgtatatattacatatatacatattgtata -ttacatatacataatacataaaatgtttaatacatacataatatatacataatataatat -tgtatattattaaattatacatgtatatatgtatac-----------atgtatacaaaat -atgtatataatatatacaaaaa-atgtgtatttttgtacatatattgtacaaaaatatgt -atattatatatacaaaatatgtatataatatatacatatattatgtaatataatatatac -ataatgtgtattacatacattatatgtaatatatacatatatattatatacatatatat- -tatata-catatatgtatatattatatacatatatgtatatattatatattatgtataca -catatgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatatt -atatattatgtatacacatatgtatatatgtatatattatatattatgtatacacatatg -tatatatgtatatattatatattatgtatacatatatgtatatatgtatatattatatat -tatgtatacatatatgtatatatgtatatattatatattatgtatacatatatgtatat- --------attatatattatgtatacatatatgtatatattatatattatgtatacatata -tgtatatattatatattatgtatacatatatgtatatattatatattatgtatacatata -tgtatatatgtatgtatacatgtatatacatatatacgtatacacatatatacgtgtata -tacatatatacgtatatacacgtatatattaaatgataaatttatatgtatatatgcgtg -tgtgcacacacacacgagatatgttggttttgtgtaatgcaaccaaataaattaagtata -cataggagagagtcactgccctgactcttaaatgtaacccttattaaagaaaatatttta -gttcattttttatctatcaaccttttttatctatcaactctgaaatctgcaatcaatcat -atttggtta diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_26a93ed6f033e25f96858d0e8ea4e5c8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_26a93ed6f033e25f96858d0e8ea4e5c8.msa deleted file mode 100644 index a0be2b0f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_26a93ed6f033e25f96858d0e8ea4e5c8.msa +++ /dev/null @@ -1,195 +0,0 @@ ->syndip_1_chr20:56280431-56282023 -aataactatcaaaaaggtaacatccatatacagatataatatctataacatatatagata -tatggatataacatccatatatagatatatctatatatctatctatagctac-------- ---------------------------------------------------------atct -acagatatctatagctacatctacagatatctatagctacatctacagatatctacagat -atctacagctacatctacagatatctatagatatctatagctatatctacagatatctat -cgatagatatatctatcgatagatatatccacatagatatctagatatatatggatatat -ctatagatatctatctggatatatctatcgatagatatatagatatatatagataaagct -atatagatatatatagataaacctatatagatacatagatatatagagagaaacctatat -acatatatagatatatagagagaaacctatatagatatatagatatatagagagaaacct -atatagatgtatagataaacctatatagatatatagataaacctatgtagatatatagat -atatatagataaatctatatagatatataaaatagataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatatatacataaatctatatatacata -aatctatatagatatatatacataaatctatatagatatatatacataaatctatataga -tatatatacataaatctatatagatatatatacataaatctatatagatatatacataaa -tctatatagatatatatacataaatctatatagatatatatacataaatctatatagata -tatatacataaatctatatagatacatatagataaatctatacagatatatagatacata -tagataaatctatacagatatatagatacatatagataaatctatacagatatatagata -catatagataaatctatacagatatatagatacatatagataaatctatacagatatata -gatacatatagataaatctatacagatatatagatacatatagataaatctatacagata -tatagatacatatagatacatctatacagatatatagatacatatagatacatctataca -gatatatagatacatatagatacatctatacagatatattgatacatatagatacatcta -tatagatatatagat--atatagatacatctatatagatatatagatatatagatacatc -tatatagatatattgatacat--atagatacatctatatagattagatatatatagatac -atctatatagattagatatatatagatacatctatatagattagatatatatagatacat -ctatatatagatatatagatatatatagatacatctatatatagacatatagatatatat -agatacatctatatatagatatatagatgtatatagatacatctatat--atagatatat -agatgtatatagatacatctatatatagatatatagatgtatatagatacatctatatat -agatatatagatgtatatagatacatctatat--atagatatatagatgtatatagatac -atctatatatagatatatagatgtatatagatacatctatatatagatatatagatgtat -atagatacatctatatatagatatatagatgtatatagatacatctatatatagatatat -agatgtatatagatacatctatatatagatatatagatgtatatagatacatagatatat -atagatacatttatgtatatatatatgtatatatagatatatagatatatatagatacat -ctacacagagagatatatagaaacatctacacagggagatatatagatacatctacatag -agagatatatagatacatctacatagagagatatatagatacatctacatagagagatat -atagatacatctacatagagagatatatagatacatctacacagagagatatatagaaac -atctacacagggagatatatagatacatctacacagagagatatatagatacatctacat -agagagatatatagatacatctacatagagagatatatagatacatctacatagagagat -atatagatacatctacatagagagatatatagatacatctacatagag ->syndip_2_chr20:56280431-56282023 -aataactatcaaaaaggtaacatccatatacagatataatatctataacatatatagata -tatggatataacatccatatatagatatatctatatatctatctatagctacatctacag -atatctatagctacatctacagatatctacagatatctatagctacatctacagatatct -acagatatctatagctacatctacagatatctatagctacatctacagatatctacagat -atctacagctacatctacagatatctatagatatctatagctatatctacagatatctat -cgatagatatatctatcgatagatatatccacatagatatctagatatatatggatatat -ctatagatatctatctggatatatctatcgatagatatatagatatatatagataaagct -atatagatatatatagataaacctatatagatacatagatatatagagagaaacctatat -acatatatagatatatagagagaaacctatatagatatatagatatatagagagaaacct -atatagatgtatagataaacctatatagatatatagataaacctatgtagatatatagat -atatatagataaatctatatagatatataaaatag------------------------a -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -tatacataaatctatatatacataaatctatatagatatatatacataaatctatataga -tatatatacataaatctatatagatatatatacataaatctatatagatatatatacata -aatctatatagatatatacataaatctatatagatatatatacataaatctatatagata -tatatacataaatctatataga------------------------tatatagatacata -tagataaatctatacagatatatagatacatatagataaatctatacagatatatagata -catatagataaatctatacagatatatagatacatatagataaatctatacagatatata -gatacatatagataaatctatacagatatatagatacatatagataaatctatacagata -tatagatacatatagataaatctatacagatatatagatacatatagatacatctataca -gatatatagatacatatagatacatctatacagatatatagatacatatagatacatcta -tacagatatattgatacatatagatacatctatatagatatatagatatatagatacatc -tata-------------------------------------------------------- ------------------------------------------tagatatatatagatacat -ctatatatagacatatagatatatatagatacatctatatatagacatatagatatatat -agatacatctatatatagatatatagatatatatagatacatctacacagagagatatat -agaaacatctacacagggagatatatagatacatctacacagagagatatatagatacat -ctacatagagagatatatagatacatctatatagagagatatatagatacatctacatag -agagatatatagatacatctacatagagagatatatagatacatctacatagagagatat -atagatacatctacatagag---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------- ->p:HG002_1_chr20:56280431-56282023 -aataactatcaaaaaggtaacatccatatacagatataatatctataacatatatagata -tatggatataacatccatatatagatatatctatatatctatctatagctacatctacag -atatctatagctacatctacagatatctacagatatctatagctacatctacagatatct -acagatatctatagctacatctacagatatctatagctacatctacagatatctacagat -atctacagctacatctacagatatctatagatatctatagctatatctacagatatctat -cgatagatatatctatcgatagatatatccacatagatatctagatatatatggatatat -ctatagatatctatctggatatatctatcgatagatatatagatatatatagataaagct -atatagatatatatagataaacctatatagatacatagatatatagagagaaacctatat -acatatatagatatatagagagaaacctatatagatatatagatatatagagagaaacct -atatagatgtatagataaacctatatagatatatagataaacctatgtagatatatagat -atatatagataaatctatatagatatataaaatagataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -tatacataaatctatatatacataaatctatatagatatatatacataaatctatataga -tatatatacataaatctatatagatatatatacataaatctatatagatatatatacata -aatctatatagatatatacataaatctatatagatatatatacataaatctatatagata -tatata--------tatatagatatatatacataaatc--------tatatagatacata -tagataaatctatacagatatatagatacatatagataaatctatacagatatatagata -catatagataaatctatacagatatatagatacatatagataaatctatacagatatata -gatacatatagataaatctatacagatatatagatacatatagataaatctatacagata -tatagatacatatagataaatctatacagatatatagatacatatagatacatctataca -gatatatagatacatatagatacatctatacagatatatagatacatatagatacatcta -tacagatatattgatacatatagatacatctatatagatatatagatatatagatacatc -tata-------------------------------------------------------- ------------------------------------------tagatatatagatata--- --tagatacatctatatagatatatatagatacatctatatatagacatatagatatatat -agatacatctatatatagatatatagatatatatagatacatctacacagagagatatat -agaaacatctacacagggagatatatagatacatctacacagagagatatatagatacat -ctacatagagagatatatagatacatctacatagagagatatatagatacatctacatag -agagatatatagatacatctacatagagagatatatagatacatctacatagag------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------- ->p:HG002_2_chr20:56280431-56282023 -aataactatcaaaaaggtaacatccatatacagatataatatctataacatatatagata -tatggatataacatccatatatagatatatctatatatctatctatagctac-------- ---------------------------------------------------------atct -acagatatctatagctacatctacagatatctatagctacatctacagatatctacagat -atctacagctacatctacagatatctatagatatctatagctatatctacagatatctat -cgatagatatatctatcgatagatatatccacatagatatctagatatatatggatatat -ctatagatatctatctggatatatctatcgatagatatatagatatatatagataaagct -atatagatatatatagataaacctatatagatacatagatatatagagagaaacctatat -acatatatagatatatagagagaaacctatatagatatatagatatatagagagaaacct -atatagatgtatagataaacctatatagatatatagataaacctatgtagatatatagat -atatatagataaatctatatagatatataaaatagataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -tatacataaatctatatatacataaatctatatagatatatatacataaatctatataga -tatatatacataaatctatatagatatatatacataaatctatatagatatatatacata -aatctatatagatatatacataaatctatatagatatatatacataaatctatatagata -tatatacataaatctatatagatatatatacataaatctatacagatatatagatacata -tagataaatctatacagatatatagatacatatagataaatctatacagatatatagata -catatagataaatctatacagatatatagatacatatagataaatctatacagatatata -gatacatatagataaatctatacagatatatagatacatatagataaatctatacagata -tatagatacatatagataaatctatacagatatatagatacatatagatacatctataca -gatatatagatacatatagatacatctatacagatatatagatacatatagatacatcta -tacagatatattgatacatatagatacatctatatagatatatagatatatagatacatc -tatatagatatatagatatatagatacatacatctatatagattagatatatatagatac -atctatatagattagatatatatagatacatctatatagattagatatatatagatacat -ctatatatagatatatagatatatatagatacatctatatatagatatatagatatatat -agatacatctatatatagatatatagatgtatatagatacatctatat--atagatatat -agatgtatatagatacatctatatatagatatatagatgtatatagatacatctatatat -agatatatagatgtatatagatacatctatat--atagatatatagatgtatatagatac -atctatatatagatatatagatgtatatagatacatctatatatagatatatagatgtat -atagatacatctatatatagatatatagatgtatatagatacatctatatatagatatat -agatgtatatagatacatctatatatagatatatagatgtatatagatacatagatatat -atagatacatttatgtatatatatatgtatatatagatatatagatatatatagatacat -ctacacagagagatatatagaaacatctacacagggagatatatagatacatctacatag -agagctatatagatatatatagatacatctatatatagacatatagatatatatagatac -atctatatatagatatatagatatatatagatacatctacacagagagatatatagaaac -atctacacagggagatatatagatacatctacacagagagatatatagatacatctacat -agagagatatatagatacatctacatagagagatatatagatacatctacatagagagat -atatagatacatctacatagagagatatatagatacatctacatagag ->ref_chr20:56280431-56282023 -aataactatcaaaaaggtaacatccatatacagatataatatctataacatatatagata -tatggatataacatccatatatagatatatctatatatctatctatagctac-------- -------------------------atctacagatatctatagctacatctacagatatct -acagatatctatagctacatctacagatatctatagctacatctacagatatctacagat -atctacagctacatctacagatatctatagatatctatagctatatctacagatatctat -cgatagatatatctatcgatagatatatccacatagatatctagatatatatggatatat -ctatagatatctatctggatatatctatcgatagatatatagatatatatagataaagct -atatagatatatatagataaacctatatagatacatagatatatagagagaaacctatat -acatatatagatatatagagagaaacctatatagatatatagatatatagagagaaacct -atatagatgtatagataaacctatatagatatatagataaacctatgtagatatatagat -atatatagataaatctatatagatatataaaatagataaatctatatagatatatataca -taaatctatatagatatatatacataaatctatatagatatatatacataaatctatata -tatacataaatctatatatacataaatctatatagatatatatacataaatctatataga -tatatatacataaatctatatagatatatatacataaatctatatagatatatatacata -aatctatatagatatatacataaatctatatagatatatatacataaatctatatagata -tatatacataaatctatatagatatatatacataaatc--------tatatagatacata -tagataaatctatacagatatatagatacatatagataaatctatacagatatatagata -catatagataaatctatacagatatatagatacatatagataaatctatacagatatata -gatacatatagataaatctatacagatatatagatacatatagataaatctatacagata -tatagatacatatagataaatctatacagatatatagatacatatagatacatctataca -gatatatagatacatatagatacatctatacagatatatagatacatatagatacatcta -tacagatatattgatacatatagatacatctatatagatatatagatatatagatacatc -tata-------------------------------------------------------- ------------------------------------------tagatatatagatata--- --tagatacatctatatagatatatatagatacatctatatatagacatatagatatatat -agatacatctatatatagatatatagatatatatagatacatctacacagagagatatat -agaaacatctacacagggagatatatagatacatctacacagagagatatatagatacat -ctacatagagagatatatagatacatctacatagagagatatatagatacatctacatag -agagatatatagatacatctacatagagagatatatagatacatctacatagag------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_26afe583378dddf4e84d652a3a398898.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_26afe583378dddf4e84d652a3a398898.msa deleted file mode 100644 index 40d5ce5e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_26afe583378dddf4e84d652a3a398898.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:64134880-64136440 -gcttctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccct -cagttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgct -ccctcagttttgtgcgtcacacacacgctccctcagttttgtgcgtc------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------acacacacgctccctcagttttgt -gcgccacaaacacgcgcactccctcagttatgtgcgtcacaaacacagacgctccctcag -ttttgcgcatcacaaacacacacgctccctcagttatggacatcacaaacacacacgctc -cctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacac -acgctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaa -acacacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgca -tcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtg -cttcacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttg -tgcgccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctca -gttttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccct -cagttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacg -ctccctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgct -ccctcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacaca -cacattccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcaca -aacacagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttca -caaacacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgt -gcatcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagtttt -gtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcag -ttttgcgcatcacacacacgctccctcagttttgtgtg---------------------- ------------tcacaaacacacacgctccctcagttgtcaggggactttgcactgtgcc -tttgcatgaaacaccatggcttgaagaggtcccgcatcgttagggcccccttgcccatgg -t ->syndip_2_chr20:64134880-64136440 -gcttctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccct -cagttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgct -ccctcagttttgtgcgtcacacacacgctccctcagttttgtgcgccacaaacacgcgca -ctccctcagttatgtgcgtcacaa------------------------------------ ------------------------------------------------------------- -------------------------------------acacagacgctccctcagttttgc -gcatcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcag -ttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacgctc -cctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacac -acgctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaa -acacacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgca -tcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtg -cttcacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttg -tgcgccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctca -gttttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccct -cagttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacg -ctccctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgct -ccctcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacaca -cacattccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcaca -aacacagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttca -caaacacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgt -gcatcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagtttt -gtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcag -ttttgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccctc -agttttgcgcatcacaaacacacacgctccctcagttgtcaggggactttgcactgtgcc -tttgcatgaaacaccatggcttgaagaggtcccgcatcgttagggcccccttgcccatgg -t ->p:HG002_1_chr20:64134880-64136440 -gcttctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccct -cagttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgct -ccctcagttttgtgcgtcacacacacgctccctcagttttgtgcgccacaaacacgcgca -ctccctcagttatgtgcgtcacaa------------------------------------ ------------------------------------------------------------- -------------------------------------acacagacgctccctcagttttgc -gcatcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcag -ttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacgctc -cctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacac -acgctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaa -acacacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgca -tcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtg -cttcacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttg -tgcgccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctca -gttttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccct -cagttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacg -ctccctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgct -ccctcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacaca -cacattccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcaca -aacacagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttca -caaacacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgt -gcatcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagtttt -gtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcag -ttttgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccctc -agttttgcgcatcacaaacacacacgctccctcagttgtcaggggactttgcactgtgcc -tttgcatgaaacaccatggcttgaagaggtcccgcatcgttagggcccccttgcccatgg -t ->p:HG002_2_chr20:64134880-64136440 -gcttctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccct -cagttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgct -ccctcagttttgtgcgtcacacacacgctccctcagttttgtgcgcc------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------acacacacgctccctcagttttgt -gcttcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcag -ttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacgctc -cctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacac -acgctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaa -acacacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgca -tcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtg -cttcacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttg -tgcgccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctca -gttttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccct -cagttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacg -ctccctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgct -ccctcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacaca -cacattccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcaca -aacacagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttca -caaacacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgt -gcatcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagtttt -gtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcag -ttttgcgcatcacacacacgctccctcagttttgtgtg---------------------- ------------tcacaaacacacacgctccctcagttgtcaggggactttgcactgtgcc -tttgcatgaaacaccatggcttgaagaggtcccgcatcgttagggcccccttgcccatgg -t ->ref_chr20:64134880-64136440 -gcttctcctctttccggtccttgacagtgattccgtgcatcacaaacacacacgctccct -cagttacacgaatcacaaacacacgctccctcagttttgtgcatcacaaacgcacacgct -ccctcagttttgtgcgtcacacacacgctccctcagttttgtgcgccacaaacacgcgca -ctccctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaaca -cacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttca -caaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgt -gcttcacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcag -ttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacacacgctc -cctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaaacacac -acgctccctcagttttgtgcttcacaaacacacacgctccctcagttatggacatcacaa -acacacacgctccctcagttttgtgcgtcacaaacacagacgctccctcagttttgcgca -tcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccttcagttttgtg -cttcacaaacacacacgctccctcagttttgtgcatcacacacacattccctcagttttg -tgcgccacaaacacgcgcgctccctcagttttgtgcatcacaaacgcacatgctccctca -gttttgggcatcacaaacacattccctcagttttgtgcatcacaaacgcacacgctccct -cagttttgtgcgtcacaaacacacacgctacctcagttttgtgtgttacaaacacacacg -ctccctcagtttcgtgcatcccaaacatgctccctcagttatgtgcgtcacaaacacgct -ccctcagttttgtgtgtcacaaacacacacgctccctcagttttgtgcatcacaaacaca -cacattccctcagttttgtgcgtcacaaacacgcgtgctctctcagttatgtgcgtcaca -aacacagacgctccctcagttttgcgcatcacacacacgctccctcagctttgtgcttca -caaacacacacgctccctcagttttgtgtgttacaaacacacacgctccctcagtttcgt -gcatcccaaagacgattcctcagttttgtgcatcacaaacacatatgctccctcagtttt -gtgcgtcacaaacgcgcgctccctcagttatgtgcgtcacaaacacagacgctccctcag -ttttgcgcatcacacacacgctccctcagttttgtgtgtcacaaacacacacgctccctc -agttttgcgcatcacaaacacacacgctccctcagttgtcaggggactttgcactgtgcc -tttgcatgaaacaccatggcttgaagaggtcccgcatcgttagggcccccttgcccatgg -t diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2b01ba4d781cd0dddb30db4277c8ca9b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2b01ba4d781cd0dddb30db4277c8ca9b.msa deleted file mode 100644 index 4bc15bf6..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2b01ba4d781cd0dddb30db4277c8ca9b.msa +++ /dev/null @@ -1,190 +0,0 @@ ->syndip_1_chr20:55624382-55625907 -atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg -cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc -cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat -actatattatataatatactataatatatataatatagtatatattgtatataatatagt -atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct -agtatactatattatatagtataactattataatatttatagtatattatactatataat -acagtatactgtattatatactataatctactagattataatatactatataatcagtat -actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat -tatagtaatatagtataatatactatacattatatagtatagtatattatatagtatact -atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat -acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta -tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact -atataatatactatattatatatactatattatatatactacactatattatatatacta -tattatatatactatactatacataaaatactatatatagtatattatatatagtatact -atatatagtatatatagtatactatatatactatatatagtatactatatagtatactat -atatagtatatatagtatactatatatagtatactatatatagtatatatatagtatact -atatatagtatactatatatagtatatatagtatactatatatagtatactatatatagt -atatatagtatactatatatagtatactatatatagtatatatagtatactatatatagt -atactatatatagtatatatagtatactatatatagtatatatagtatactatatatagt -atatatagtatactatatatactatatatactatatatagtatactatatatagtatata -tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac -tatactataatatactatttgttataattatctagtatagtatactatatatactatatt -atatagtatatagtatatatagtatatttatagtatatatactatatactatatatacta -tatactataatatatactatatatactaaataaatataatatacttatttaaatatattt -aaataaatata--aaatatttaaatataattacttaaatatatatttaaaatatttaata -aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt -atatatatattatatactatatattatatatact-----atatactatatatagtatact -aatataatatactatatatactatatataatatactatatatagtatatatagtatagta -tactataatatactatat-------------------------------------tatat -aatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta -tagtatactgtatactatac-----tatacagtatactgtatactatactatagta---- ----------tacagtatactatatactattgtatagtatatagtatactgtatactatag -tatagtatactatatactatactatactatagtatactctatagtatataaagacatata -tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat -acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa -tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatc ->syndip_2_chr20:55624382-55625907 -atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg -cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc -cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat -actatattatataatatactataatatatataatatagtatatattgtatataatatagt -atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct -agtatactatattatatagtataactattataatatttatagtatattatactatataat -acagtatactgtattatatactataatctactagattataatatactatataatcagtat -actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat -tatagtaatatagtataatatactatac-----------------attatatagtatact -atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat -acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta -tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact -atataatat---------------------------------actatattatatatacta -tattatatatactatactatacataaaatactatatatagtatat--------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------tatatatagtatactatatatagtatata -tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac -tatactataatatactatttgttataattatctagtatagtatactatatatactatat- -------tatatagtatatatagtatatttatagtatatatactatatactatatatacta -tataatataatatataatatatatactaaata-----aatatacttatttaaatatattt -aaataaatatattaaatatttaaatataattacttaaatatatatttaaaatatttaata -aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt -atatatatattatatactatatattatatatactatataatatactatatatagtatact -aatataatatactatatatactatatataatatactatatatagtatatatagtatagta -tactataatatactatatatagtatatatagtatagtatactataatatactatatatag -tatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta -tagtatactgtatactatactatagtatacagtatactatatactatactatagtatagt -atactatagtatagtatactatatactatactatagtatatagtatactgtatac----- -tatagtatactatatactatactatactatagtatactctatagtatataaagacatata -tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat -acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa -tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatc ->p:HG002_1_chr20:55624382-55625907 -atcccagctacttgggaggctgaggcaggataatcacttcaatcagtgaggtggaggctg -cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc -cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat -actatattatataatatactataatatatataatatagtatatattgtatataatatagt -atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct -agtatactatattatatagtataactattataatatttatagtatattatactatataat -acagtatactgtattatatactataatctactagattataatatactatataatcagtat -actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat -tatagtaatatagtataatatactatac-----------------attatatagtatact -atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat -acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta -tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact -atataatat---------------------------------actatattatatatacta -tattatatatactatactatacataaaatactatatatagtatat--------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------tatatatagtatactatatatagtatata -tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac -tatactataatatactatttgttataattatctagtatagtatactatatatactatat- -------tatatagtatatatagtatatttatagtatatatactatatactatatatacta -tataatataatatataatatatatactaaata-----aatatacttatttaaatatattt -aaataaatatattaaatatttaaatataattacttaaatatatatttaaaatatttaata -aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt -atatatatattatatactatatattatatatactatataatatactatatatagtatact -aatataatatactatatatactatatataatatactatatatagtatatatagtatagta -tactataatatactatatatagtatatatagtatagtatactataatatactatatatag -tatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta -tagtatactgtatactatactatagtatacagtatactatatactatactatagtatagt -atactatagtatagtatactatatactatactatagtatatagtatactgtatac----- -tatagtatactatatactatactatactatagtatactctatagtatataaagacatata -tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat -acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa -tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatc ->p:HG002_2_chr20:55624382-55625907 -atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg -cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc -cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat -actatattatataatatactataatatatataatatagtatatattgtatataatatagt -atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct -agtatactatattatatagtataactattataatatttatagtatattatactatataat -acagtatactgtattatatactataatctactagattataatatactatataatcagtat -actatattatatagtatagtataatatagtattatattatagtaatatattataaagtat -tatagtaatatagtataatatactatacattatatagtatagtatattatatagtatact -atatataagtatatataatagtatattgtatatagtaattatatatagtatatataatat -acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta -tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact -atataatatactatattatatatactatattatatatactacactatattatatatacta -tattatatatactatactatacataaaatactatatatagtatattatatatagtatact -atatatagtatatatagtatactatatatactatatatagtatactatatagtatactat -atatagtatatatagtatactatatatagtatactatatatagtatatatatagtatact -atatatagtatactatatatagtatatatagtatactatatatagtatactatatatagt -atatatagtatactatatatagtatactatatatagtatatatagtatactatatatagt -atactatatatagtatatatagtatactatatatagtatatatagtatactatatatagt -atatatagtatactatatatactatatatactatatatagtatactatatatagtatata -tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac -tatactataatatactatttgttataattatctagtatagtatactatatatactatatt -atatagtatatagtatatatagtatatttatagtatatatactatatactatatatacta -tatactataatatatactatatatactaaataaatataatatacttatttaaatatattt -aaataaatata--aaatatttaaatataattacttaaatatatatttaaaatatttaata -aacatatatttaaatatttatttaatatttaaatattaaatatatataattaatataatt -atatatatattatatactatatattatatatact-----atatactatatatagtatact -aatataatatactatatatactatatataatatactatatatagtatatatagtatagta -tactataatatactatat-------------------------------------tatat -aatatagtatactatatattgtatactatactatgctatagtatgctatatactacacta -tagtatactgtatactatac-----tatacagtatactgtatactatactatagta---- ----------tacagtatactatatactattgtatagtatatagtatactgtatactatag -tatagtatactatatactatactatactatagtatactctatagtatataaagacatata -tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat -acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa -tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatc ->ref_chr20:55624382-55625907 -atcccagctacttgggaggctgaggcaggagaatcacttcaatcagtgaggtggaggctg -cagtgggccaagatcatgcgattgcaccccagcctgggtaagaaagtgaggtcctgtctc -cctgtctctcatatatatacataactaaaataatatatagtaatatatgttatatattat -actatattatataatatactataatatatataatatagtatatattgtatataatatagt -atatataatataatagtatataatatagtatagatagtatagaatatatagtatatacct -agtatactatattatatagtataactattataatatttatagtatattatactatataat -acagtatactgtattatatactataatctactagattataatatactatataatcagtat -actatatt-----gtatagtataatatagtattatattatagtaatatattataaagtat -tatagtaatatagtataatatactatacattatatagtatagtatattatatagtatact -atatataagtatatttaatagtatattgtatatagtaattatatatagtatatataatat -acaatgtatagtatattatagtatactatacgatactgtagtatagtatgctatatagta -tactatatacgacagtatcatatagtatactacaaaatatatagtatagcatagtatact -atataatatactatattatatatactatattatatatactatactatattatatatacta -tattatatatactatactatacataaaatactatatatagtatattatatatagtatact -atatatagtatataatatata--------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------gtatactatatatactatatatagtatactatatatactatata -tagtatactatatatcatatatagtattatatacagtatactatatataatatagtatac -tatactataatatactatttgttataattatctagtatagtatactatatatactatatt -atatagtatatagtatatatagta----tatagtatatatactatatactatatatacta -tatactatactatataatatatatacta-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------atatattgtatactatactatgctatagtatgctatatactacacta -tagtatactgtgtactatactatagtatacagtatactatatactatactatagtatagt -atactatagtatagtatactatatactatagtatagtatatagtatactgtatactatag -tatagtatactatatactatactatactatagtatactctatagtatataaagacatata -tatagtcttcaaaatgaagatcctgtatcctatatatatatataacttcaaaagtgagat -acatatatatgatgtagaaactttagaatatacaaaattgtcttcttcaggataagaaaa -tcctgatattcagcctaacctccactgactgtaaaggaagaatgggtttcactttcaggg -aaggtcaccttcatc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2c05a87978c7b4aa656e86b640a18690.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2c05a87978c7b4aa656e86b640a18690.msa deleted file mode 100644 index 6bac5dcb..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2c05a87978c7b4aa656e86b640a18690.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:63027897-63028266 -acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg -ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa -gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggtg -gggagaggaccggtggggagggggccggtggagagggggccggtggggagggggccggtg -gggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtgg -ggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtgggg -agggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtgggg -agggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggga -gggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggaggg -ggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagcg -tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg ->syndip_2_chr20:63027897-63028266 -acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg -ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa -gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg -ggga----------------ggggccggtggagagggggccggtggggagggggccggcg -gggag--------------tggtttggtggggagggggccggtggggagggggcctgcgg -ggaggggccggtggggag-----------------------------ggggccggtgggg -agggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtgggg -ag-----------------------------ggggccggtggggagggggccggcgggga -gggggccggcggggaggggccggtggggagtggtctg----------------------- --------------------gtggggagggggccggtggggaggaggctggtgaagtagcg -tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg ->p:HG002_1_chr20:63027897-63028266 -acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg -ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa -gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg -ggga----------------ggggccggtggagagggggccggtggggagggggccggcg -gggag--------------tggtttggtggggagggggccggtggggagggggcctgcgg -ggaggggccggtggggag-----------------------------ggggccggtgggg -agggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtgggg -ag-----------------------------ggggccggtggggagggggccggcgggga -gggggccggcggggaggggccggtggggagtggtctg----------------------- --------------------gtggggagggggccggtggggaggaggctggtgaagtagcg -tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg ->p:HG002_2_chr20:63027897-63028266 -acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg -ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa -gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggtg -gggagaggaccggtggggagggggccggtggagagggggccggtggggagggggccggtg -gggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtgg -ggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtgggg -agggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtgggg -agggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggga -gggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggaggg -ggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagcg -tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg ->ref_chr20:63027897-63028266 -acggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgtg -ctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtgaa -gaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggtg -ggga----------------ggggccggtggagagggggccggtggggagggggccggcg -gggag--------------tggttt----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------ggtggggaggaggctggtgaagtagcg -tcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgca -gcttcatcaggttctcaattagcggagggcgctggcggtggaggaggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2d77298b514346b1a545eb7250237cce.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2d77298b514346b1a545eb7250237cce.msa deleted file mode 100644 index db86ad1e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2d77298b514346b1a545eb7250237cce.msa +++ /dev/null @@ -1,125 +0,0 @@ ->syndip_1_chr20:641735-642566 -gatcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccc -tgccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtg -ccccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctggggggggg -ggcccagcgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctggg -ggggggaggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagtt -gcctggg-----------------------------ggggggaggcccagcgggggtgga -gttgcctgggggggggcccagcgggggtggagttgcctgggggggg-ggcccagcggggg -tggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg--gccca -gcgggggtggagttgcctgggg---------------------------gggggaggccc -agcgggggtggagttgcctgggggggg-------------------------------gg -cccagcgggggtggagttgcctg-gggggg---ggcccagcgggggtggagttgcctggg -ggggg---cccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct -g-gggggggccccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagt -tgcctgggggggg--gcccagcgggggtggagttgcctggggggggcccagcgggggtgg -agttgcctggggggggccccagcgggggtggagttgcctgggggggggcccagcgggggt -ggagttgcctggggggggggcccagcgggggtggagttgcctggggggggggcccagcgg -gggtggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggggccca -gcgggggtggagttgcctg-gggggggggcccagcgggggtggagttgcct-gggggggg -cccagcgggggtggagttgcct-gggggggggcccagcgggggtggagttgcctg-gggg -gggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgt -gggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcc -tgggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcggga -ggcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggct -gtcgggcggggggcggcgctcgcagttccggaggggg ->syndip_2_chr20:641735-642566 -gatcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccc -tgccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtg -ccccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-gggggggg -ggcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctggg -ggggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagtt -gcctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtgga -gttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcggggg -tggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgccca -gcgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggccc -agcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggggggagg -cccagcgggggtggagttgcctg-ggggggggaggcccagcgggggtggagttgcctggg -ggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcct -g-ggggggg-cccagcgggggtggggttgcctggggggggaggcccagcaggggtggagt -tgcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtgg -agttgcctgggggggg-cccagcgggggtggagttgcctgggggggggcccagcggggat -ggggttgcct-gggggggggcccagcgggggtggggttgcct-gggggggggcccagcgg -gggtggagttgcct--gggggggggcccagcgggggtggagttgcct-ggggggggccca -gcgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctggggggggg -cccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgtggtg -gggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgt -gggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcc -t-ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcggga -ggcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggct -gtcgggcggggggcggcgctcgcagttccggaggggg ->p:HG002_1_chr20:641735-642566 -gatcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccc -tgccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtg -ccccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-gggggggg -ggcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctggg -ggggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagtt -gcctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtgga -gttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcggggg -tggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgccca -gcgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggccc -agcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggggggagg -cccagcgggggtggagttgcctg-ggggggggaggcccagcgggggtggagttgcctggg -ggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcct -g-ggggggg-cccagcgggggtggggttgcctggggggggaggcccagcaggggtggagt -tgcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtgg -agttgcctgggggggg-cccagcgggggtggagttgcctgggggggggcccagcggggat -ggggttgcct-gggggggggcccagcgggggtggggttgcct-gggggggggcccagcgg -gggtggagttgcct--gggggggggcccagcgggggtggagttgcct-ggggggggccca -gcgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctggggggggg -cccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgtggtg -gggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgt -gggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcc -t-ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcggga -ggcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggct -gtcgggcggggggcggcgctcgcagttccggaggggg ->p:HG002_2_chr20:641735-642566 -gatcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccc -tgccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtg -ccccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctggggggggg -ggcccagcgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctggg -ggggggaggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagtt -gcctggg-----------------------------ggggggaggcccagcgggggtgga -gttgcctgggggggggcccagcgggggtggagttgcctgggggggg-ggcccagcggggg -tggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg--gccca -gcgggggtggagttgcctgggg---------------------------gggggaggccc -agcgggggtggagttgcctgggggggg-------------------------------gg -cccagcgggggtggagttgcctg-gggggg---ggcccagcgggggtggagttgcctggg -ggggg---cccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct -g-gggggggccccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagt -tgcctgggggggg--gcccagcgggggtggagttgcctggggggggcccagcgggggtgg -agttgcctggggggggccccagcgggggtggagttgcctgggggggggcccagcgggggt -ggagttgcctggggggggggcccagcgggggtggagttgcctggggggggggcccagcgg -gggtggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggggccca -gcgggggtggagttgcctg-gggggggggcccagcgggggtggagttgcct-gggggggg -cccagcgggggtggagttgcct-gggggggggcccagcgggggtggagttgcctg-gggg -gggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgt -gggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcc -tgggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcggga -ggcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggct -gtcgggcggggggcggcgctcgcagttccggaggggg ->ref_chr20:641735-642566 -gatcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccc -tgccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtg -ccccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-gggggggg -ggcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctggg -ggggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagtt -gcctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtgga -gttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcggggg -tggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgccca -gcgggggtggagttgcct------------------------------------------ ----------------------gggggg-------------------------------gg -cccagcgggggtggagttgcctgtggtggg---gggccagcgggggtgaagttgcctggg -ggggg----ccagcgggggtggagttgcctgggggggggccagcgggggtggagttgcct -gtgggggggggccagcgggggtggagttgcctgggggggg----ccagcgggggtggagt -tgcctgggggggg----ccagcgggggtggagcaccctggacggcccc--------gcgg -agccccctgcgggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaa -gacattacacggctgtcgggcggggggcggcgctcgcagttccggaggggg--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2df0f23155fe6490259f222945f7f88b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2df0f23155fe6490259f222945f7f88b.msa deleted file mode 100644 index 42c76216..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2df0f23155fe6490259f222945f7f88b.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:20295904-20296440 -cccctgcagccagaggctcagtcctggctttttccaaactcttctccagaggagcccgcc -cttgcacaccaacgcctgcatgcttccctccttccttccttccttccctcctttccttcc -ttctttcttttcttcctccctcccttcct---tcccttccttcccttccttccctccttt -tcttccttctttccttccttccttccctccctccttcccttccttccttccttcccttcc -ttccttctctccttccttccttccctccctccttcccttccttccttctctccttccttc ---ccttccttccttctctccttccttcccttccttccttctctccttccttcccttcctt -ccttctctccttccttcccttccttccttctctccttccttcccttgctt--cctttctt -ccttcctttgcttccttgcttccttctttcctttcttcatccctccctccctccttcctt -cctttccttccttccctctatccttccttccttcctttctttctccctcccttccttccc -ttccttccttccctcttttccttccatctttcctttcttcctccctccctccctccttcc -ctccttcattccttccttccctcctttccttccttcacctccttcccttctctcctccct -tcatcccttccttcctttcttccttccctccctcttccttcctttcttcacccctccccc -ttccctcatcccttccctccttcccttccttccttccttccctccttccttcccttcctt -ccttccttgcttccttccttctttcctttcttcatccctccttccctccctccctccttc -ctgccttccttctttctttcttttctttcttcctccctccctcctt ->syndip_2_chr20:20295904-20296440 -cccctgcagccagaggctcagtcctggctttttccaaactcttctccagaggagcccgcc -cttgcacaccaacgcctgcatgcttccctccttccttccttccttccctcct-tccttcc -ttccttccttccttcctgcctgcctgcctgccttcctgccttcccttcctccctccc--t -ccctacctccctccctccttccttcccttcctccctccctcccttctttacttccttcc- -------tccttccctcctcctttcctccatccttccctcccttctttcctttcttcctcc -tgccctccctccttctttcccttcctccctcccttccttcccatcctccttccc-tccct -ccttccttcctgccttccttccttccctccatccttccttccttcctttcttcctccctc -ccttccttcctcccttccttcccttccttcct-----------tccctcttttccttcca -tctttcctttcttcctccctccctccctccttccctccttcattccttccttccctcctt -tccttccttcacctccttcccttctctcctcccttcatcccttccttcctttcttccttc -cctccctcttccttcctttcttcacccctcccccttccctcatcccttccctccttccct -tccttccttccttccctccttccttccct---tccttccttccttccctccttccttccc -ttccttccttgcttccttccttccttcccttccttccttgcttccttccttccttccctt -ccttccttgcttccttccttctttcctttcttcatccctccttccctccctccctccttc -ctgccttccttctttctttcttttctttcttcctccctccctcctt ->p:HG002_1_chr20:20295904-20296440 -cccctgcagccagaggctcagtcctggctttttccaaactcttctccagaggagcccgcc -cttgcacaccaacgcctgcatgcttccctccttccttccttccttccctcct-tccttcc -ttccttccttccttcctgcctgcctgcctgccttcctgccttcccttcctccctccc--t -ccctacctccctccctccttccttcccttcctccctccctcccttctttacttccttcc- -------tccttccctcctcctttcctccatccttccctcccttctttcctttcttcctcc -tgccctccctccttctttcccttcctccctcccttccttcccatcctccttccc-tccct -ccttccttccttctttcttttcttcctccctcccttccttcccttccttc--ccttcctt -ccctccttttcttccttctttccttccttcct-----------tccctccctccttccct -tccttccttccttcctccctccctccctccttccctccttcattccttccttccctcctt -tccttccttcacctccttcccttctctcctcccttcatcccttccttcctttcttccttc -cctccctcttccttcctttcttcacccctcccccttccctcatcccttccctccttccct -tccttccttccttccctccttccttccct---tccttccttccttccctccttccttccc -ttccttccttgcttccttccttccttcccttccttccttgcttccttccttccttccctt -ccttccttgcttccttccttctttcctttcttcatccctccttccctccctccctccttc -ctgccttccttctttctttcttttctttcttcctccctccctcctt ->p:HG002_2_chr20:20295904-20296440 -cccctgcagccagaggctcagtcctggctttttccaaactcttctccagaggagcccgcc -cttgcacaccaacgcctgcatgcttccctccttccttccttccttccctcctttccttcc -ttctttcttttcttcctccctcccttcct---tcccttccttcccttccttccctccttt -tcttccttctttccttccttccttccctccctccttcccttccttccttccttcccttcc -ttccttctctccttccttccttccctccctccttcccttccttccttctctccttccttc ---ccttccttccttctctccttccttcccttccttccttctctccttccttcccttcctt -ccttctctccttccttcccttccttccttctctccttccttcccttgctt--cctttctt -ccttcctttgcttccttgcttccttctttcctttcttcatccctccctccctccttcctt -cctttccttccttccctctatccttccttccttcctttctttctccctcccttccttccc -ttccttccttccctcttttccttccatctttcctttcttcctccctccctccctccttcc -ctccttcattccttccttccctcctttccttccttcacctccttcccttctctcctccct -tcatcccttccttcctttcttccttccctccctcttccttcctttcttcacccctccccc -ttccctcatcccttccctccttcccttccttccttccttccctccttccttcccttcctt -ccttccttgcttccttccttctttcctttcttcatccctccttccctccctccctccttc -ctgccttccttctttctttcttttctttcttcctccctccctcctt ->ref_chr20:20295904-20296440 -cccctgcagccagaggctcagtcctggctttttccaaactcttctccagaggagcccgcc -cttgcacaccaacgcctgcatgcttccctccttccttccttccttccctcctttccttcc -ttctttcttttcttcctccctcccttcct---tcccttccttc----------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------ccttcctt -ccctccttttcttccttctttccttccttcct-----------tccctccctccttccct -tccttccttccttcctccctccctccctccttccctccttcattccttccttccctcctt -tccttccttcacctccttcccttctctcctcccttcatcccttccttcctttcttccttc -cctccctcttccttcctttcttcacccctcccccttccctcatcccttccctccttccct -tccttccttccttccctccttccttccct------------------------------- --------------------------------------------------------tcctt -ccttccttgcttccttccttctttcctttcttcatccctccttccctccctccctccttc -ctgccttccttctttctttcttttctttcttcctccctccctcctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2e395a6e1327c3cee2e68d6b7c844cc7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2e395a6e1327c3cee2e68d6b7c844cc7.msa deleted file mode 100644 index 13fdbb64..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2e395a6e1327c3cee2e68d6b7c844cc7.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:5039849-5040599 -agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt -gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg -tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat -ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg -ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa -gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg -tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc -agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctca -aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta -gcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcct -gggcaacatagggagaacttgtctctattt------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct -caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagccttt ->syndip_2_chr20:5039849-5040599 -agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt -gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg -tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat -ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg -ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa -gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg -tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc -agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc- -aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta -gcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcct -gggcaacatagggagaacttgtctctattt------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct -caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagccttt ->p:HG002_1_chr20:5039849-5040599 -agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt -gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg -tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat -ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg -ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa -gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg -tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc -agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc- -aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta -gcactctttgggaggctgagactggaggatcttttgagcccaggggtttgagaccagcct -gggcaacatagggagaacttgtctctatttaaaaaaaaaggccgggcgcggtggctcacg -cctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtcaggagatcgag -accatcctggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccggg -cgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagtg -agccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgtc -tcaaaaaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct -caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagccttt ->p:HG002_2_chr20:5039849-5040599 -agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt -gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg -tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat -ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg -ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa -gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg -tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc -agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctca -aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta -gcactctttgggaggctgagactggaggatcttttgagcccaggggtttgagaccagcct -gggcaacatagggagaacttgtctctattttaaaaaaaaggccgggcgcggtggctcacg -cctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtcaggagatcgag -accatcctggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccggg -cgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagtg -agccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgtc -tc---aaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct -caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagccttt ->ref_chr20:5039849-5040599 -agacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatgt -gagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacagg -tattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagcat -ttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtactttg -ggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaaa -gtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgttg -tcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagcttc -agttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc- -aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctta -gcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcct -gggcaacatagggagaacttgtctctattt------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcct -caaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggca -acccggattagccttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2eef9ad3848c82aa14b84e6b16eed43b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2eef9ad3848c82aa14b84e6b16eed43b.msa deleted file mode 100644 index 73859228..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2eef9ad3848c82aa14b84e6b16eed43b.msa +++ /dev/null @@ -1,45 +0,0 @@ ->syndip_1_chr20:16395091-16395483 -catacccctgtcatcggtgtcttcttactctctccctaatgtgatgtattcatcctccca -gtttagtcaaggcagaaaggagatgaggaaggggagaggaggggagaggagggaagagga -ggggaggggaggggagaggaggagaggggaggagaggggaggccaagggaggggagggga -ggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaaggga -ggggaggggaggggaggagaggggaggccaagggaggggaggggaggagaggggaggcca -agggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggaggaga -ggggaggccaagggagaagatatgaaagaaatagggaaggagtgggacacagggaggaaa -acaaaactatttcctttcatataaatgttgtcatctggggagaagccc ->syndip_2_chr20:16395091-16395483 -catacccctgtcatcggtgtcttcttactctctccctaatgtgatgtattcatcctccca -gtttagtcaaggcagaaaggagatgaggaaggggagaggaggggagaggaggggag---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------gggaggggaggggagagga -ggggaggccaagggagaagatatgaaagaaatagggaaggagtgggacacagggaggaaa -acaaaactatttcctttcatataaatgttgtcatctggggagaagccc ->p:HG002_1_chr20:16395091-16395483 -catacccctgtcatcggtgtcttcttactctctccctaatgtgatgtattcatcctccca -gtttagtcaaggcagaaaggagatgaggaaggggagaggaggggagaggagggaag---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------gggaggggaggggaggaga -ggggaggccaagggagaagatatgaaagaaatagggaaggagtgggacacagggaggaaa -acaaaactatttcctttcatataaatgttgtcatctggggagaagccc ->p:HG002_2_chr20:16395091-16395483 -catacccctgtcatcggtgtcttcttactctctccctaatgtgatgtattcatcctccca -gtttagtcaaggcagaaaggagatgaggaaggggagaggaggggagaggagggaagagga -ggggaggggaggggagaggaggagaggggaggagaggggaggccaagggaggggagggga -ggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaaggga -ggggaggggaggggaggagaggggaggccaagggaggggaggggaggagaggggaggcca -agggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggaggaga -ggggaggccaagggagaagatatgaaagaaatagggaaggagtgggacacagggaggaaa -acaaaactatttcctttcatataaatgttgtcatctggggagaagccc ->ref_chr20:16395091-16395483 -catacccctgtcatcggtgtcttcttactctctccctaatgtgatgtattcatcctccca -gtttagtcaaggcagaaaggagatgaggaaggggagaggaggggagaggagggaagagga -ggggaggggaggggagaggaggagaggggaggagaggggaggccaagggaggggagggga -ggggaggagaggggaggccaa-----gggaggggaggggaggagaggggaggccaaggga -ggggaggggaggggaggagaggggaggccaa----------------------------- ------------------------------------------gggaggggaggggaggaga -ggggaggccaagggagaagatatgaaagaaatagggaaggagtgggacacagggaggaaa -acaaaactatttcctttcatataaatgttgtcatctggggagaagccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_2f05294de09cdef4b85e1df116ec0a11.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_2f05294de09cdef4b85e1df116ec0a11.msa deleted file mode 100644 index 5d4b9da6..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_2f05294de09cdef4b85e1df116ec0a11.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:57350746-57351030 -gggttcaagcgattctcctgccttagcctcccaagcagctgggattacaggcacccgcca -ccatgcccggctaatttttgtatttttagtactgacggggggacgggggggcgggggacg -ggggacggggggcgggggggacgggggacggggggcggggggggcgggggggacgggggg -cggggggggcgggggccggggggggcggggggacgggggcggggggccgg-------ggg -gggcggggggacggggggcggggggggcggggggggcggggggacgggggcggggggcgc -gggggggcggggggggcggcgcgggggggcggggggggcggggggcggggcggttcacga -tgttggccagacttgtcttgaactcctgaccccaggtgatcagcccgcctcggcctcc ->syndip_2_chr20:57350746-57351030 -gggttcaagcgattctcctgccttagcctcccaagcagctgggattacaggcacccgcca -ccatgcccggctaatttttgtatttttagtactgacggggggacgggggggcg------- ------------------------------------------------------------- ----------------------------------------------------------ggg -gggcggggggacggggggcggggggggcggggggggcggggggacgggggcggggggcg- ---------ggggggggcggcgcgggggggcggggggggcggggggcggggcggttcacga -tgttggccagacttgtcttgaactcctgaccccaggtgatcagcccgcctcggcctcc ->p:HG002_1_chr20:57350746-57351030 -gggttcaagcgattctcctgccttagcctcccaagcagctgggattacaggcacccgcca -ccatgcccggctaatttttgtatttttagtactgacggggggacgggggggcg------- ------------------------------------------------------------- ----------------------------------------------------------ggg -gggcggggggacggggggcggggggggcggggggggcggggggacgggggcggggggcg- ---------ggggggggcggcgcgggggggcggggggggcggggggcggggcggttcacga -tgttggccagacttgtcttgaactcctgaccccaggtgatcagcccgcctcggcctcc ->p:HG002_2_chr20:57350746-57351030 -gggttcaagcgattctcctgccttagcctcccaagcagctgggattacaggcacccgcca -ccatgcccggctaatttttgtatttttagtactgacggggggacgggggggcgggggacg -ggggacggggggcgggggggacgggggacggggggcggggggggcgggggggacgggggg -cggggggggcgggggccggggggggcggggggacgggggcggggggccggggggggcggg -gggcggggggacggggggcggggggggcggggggggcggggggacgggggcggggggcg- ---------ggggggggcggcgcgggggggcggggggggcggggggcggggcggttcacga -tgttggccagacttgtcttgaactcctgaccccaggtgatcagcccgcctcggcctcc ->ref_chr20:57350746-57351030 -gggttcaagcgattctcctgccttagcctcccaagcagctgggattacaggcacccgcca -ccatgcccggctaatttttgtatttttagtactgacggggggacgggggggcg------- ------------------------------------------------------------- ----------------------------------------------------------ggg -gggcggggggacggggggcggggggggcggggggggcggggggacgggggcggggggcg- ---------ggggggggcggcgcgggggggcggggggggcggggggcggggcggttcacga -tgttggccagacttgtcttgaactcctgaccccaggtgatcagcccgcctcggcctcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_31322e75509c4e7a04913fb3ade580bd.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_31322e75509c4e7a04913fb3ade580bd.msa deleted file mode 100644 index edd5135b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_31322e75509c4e7a04913fb3ade580bd.msa +++ /dev/null @@ -1,385 +0,0 @@ ->syndip_1_chr20:63167286-63167728 -gaatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagtt -gctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacgg -ttcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacct -cagtgcccacctcagccccctcctcagcccccacctccgcccccacctcagcccct---- ---------------------cctcagcccccacctcagccccctcctcagcccccacctc -c-----------------------gcccccacctccgcccccacctctgcccct------ --------cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctcc -gcccccacctctgcccct-------------------------------------cctca -gcccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctct -gcccctcctcagcccccacctcagccccctcctcag-----------cccccacctccgc -cccctcctcagcccccacctctgcccct------------cctcagcccccacctcagcc -ccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgccc -ccacctcagcccccacctcc-----------------------gccccctcctcagcccc -cacctctgcccctcctcagcccccacctcagcccccacctcagcccccacctc------- ------------------------------------------------------------- ------------------------------ccccctcctcagcccccacctcagcccccac -ctcagccccctcctcagcccccacctcagcccccacctccgcccct------------cc -tcagcccccacctccgcccccacctcagcccccacctcagcccccacctccgcccccacc -tcagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacc -tctgcccctcctcagcccccacctccgccccctcctcagcccccacctctg--------- ----------------------------cccctcctcagcccccacctcagcccccacctc -agcccccacctcc-cccctcctcagcccccacctcagcccccacctcagccccctcctca -gcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcag -cccccacctccgcccctcctcagcccccacctcag------------------------- ------------------------------------------------------------- ----------ccccctcctcagcccccacctccgcccccacctccgcccccacctctgccc -ctcctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgcccc -cacctccgcccctcctccgcccccacctcagcccccacctccgccccct----------- ------------------------cctcagcccccacctctgcccctcctcagcccccacc -tcagcccccacctcagcccccacct-------------------------cccccctcct -cagcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccca---- --------------------------------------------------------cctca -gcccccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctca -gcccccacctcc-----------gcccccacctcagcccccacctctgcccctcctcagc -ccccacctccgccccctcctcagcccccacctctgcccctcctcagcccccacctcagcc -cccacctcagcccccacct-------------------------cccccctcctcagccc -cca-----------------------------------cctcagcccccacctcagcccc -ctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccccc -a-----------------------cctcagcccccacctccgcccctcctccgcccccac -ctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacc -tccgcccccacctcagccccctcctcagcccccacctc---------------------- ----------------ccccctcctccgcccccacctcagcccccacctcagcccccacct -cagcccccacctc----------------------------------------------- ------------------------------------------------------------- -ccccctcctccgcccccacctcagccccca-----------cctcagcccccacctccgc -ccccacctcagcccccacctcc-------------------------------------- ------------------------------------------------------------- ---------cccctcctcagcccccacctcagcccccacctccgccccca----------- -cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccac -ctccgcccccacctcagcccccacctcagcccccacctccgccccca------------- ---------------------------------------------------------cctc -agcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctc -cgcccccacctccgcccccacctcc-----------gcccccacctcagcccccacctca -gcccccacctccgccccca----------------------------------------- ------cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcc -cccacctcagcccctcctcagcccccacctcagcccccacctcagcccccacctcagccc -ct-------------------------cctcagcccccacctcagccccctcctcagccc -cctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagccc -cacctcagcccctcctcagcccccacctcagccc-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------cctcagccccc -acctcagcccccacctccgcccccacctccgcccccacctcc------------------ ------------------------------------------------------------- ------gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacc -tcc--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------acccccacctccgtccccacctccgccccctcctcagccccctcctcag -cccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgc -ccccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagct -gctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccg -ccacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggc -gccttgt ->syndip_2_chr20:63167286-63167728 -gaatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagtt -gctatccatcccctcgactaatacttaccaaattaattccagatttggattcactcacgg -ttcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacct -cagtgcccacctcagccccctcctcagcccccacctccgcccccacctccgccccctcct -cagcccctcctccgcccccacctcagcccccacctcagccccctcctcagcccccacctc -cgcccctcctcagcccccacctcagcccccacctcagcccccacctccgccccctcctca -gcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcc -gcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctca -gcccccacctcagccccctcctcagcccccacctcagcccccacctccgccccctcctca -gcccccacctcccccccacctccgccccctcctcagcccccacctcccccccacctccgc -cccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctcagcc -ccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccc -ccacctcagcccccacctccgcccctcctctgcccccacctcagccccctcctcagcccc -cacctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagccccc -acctcagcccccacctccccccctcctcagcccccacctccacccccacctcagccccca -cctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccac -ctccgcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacc -tcagcccccacctccgcccccacctccgcccccacctcagcccccacctccgccccctcc -tcagcccccacctcagcccccacctcagcccccacctccacccccacctcagcccccacc -tcagcccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctc -aggccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctc -agcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctca -gcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcag -cccccacctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgc -ccctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagcc -cccacctccccccctcctcagcccccacctccacccccacctcagcccccacctccgccc -ctcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgcccc -cacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagccccca -cctccgcccctcctcagcccccacctcagcccccacctccgcccctcctcagcccccacc -tcagcccccacctccacccccacctcagcccccacctcagcccccacctcccccccacct -ccgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctc -agccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctca -gcccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacctca -gcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgc -ccccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcc -cccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcagccc -ccacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagcccc -cacctccacccccacctcagcccccacctcagcccccacctccgcccctcctcagccccc -acctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccac -ctccgcccccacctcagccccctcctccgcccctcctcagcccccacctccacccccacc -tcagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacct -cagcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacct -cagccccctcctccacccctcctcagcccccacctccgcccccacctcagcccccacctc -cgcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcctcag -cccccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctccgc -ccccacctcagcccccacctccgcccctcctcagcccccacctccacccccacctcagcc -cccacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccc -cacctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccccccct -cctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccac -ctcagcccccacctccacccccacctcagcccccacctcagcccccacctccgcccctcc -tcagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctc -agcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctc -cgcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctca -gaccccacctccgcccccacctccgcccctcctcagcccccacctcagcccccacctcag -cccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctcagcc -cccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagccc -ccacctcagcccccacctccgcccccacctcagccccctcctcagcccccacctcagccc -cctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagccc -cacctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccctc -ctcagcccccacctcagccccctcagcccccacctcagcccccacctccgcccccacctc -cgcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccg -cccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctcagc -cccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctcagcc -cctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcctcagccccc -acctcagcccccacctccgcccccacctccgcccccacctccgcccccacctcagcccct -cctcagcccccacctcagcccccacctcagccccctcctcagcccccacctccgccccca -cctcagcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacc -tccgcccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacct -cagccccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctc -agcccctcctcagcccccacctcagcccctcctcagccccctcctcagcccccacctcag -cccccacctcagcccccacctccgcccccacctccgcccccacctcagccccctcctcag -ccccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgc -ccccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagct -gctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccg -ccacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggc -gccttgt ->p:HG002_1_chr20:63167286-63167728 -gaatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagtt -gctatccatcccctcgactaatacttaccaaattaattccagatttggattcactcacgg -ttcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacct -cagtgcccacctcagccccctcctcagcccccacctccgcccccacctccgccccctcct -cagcccctcctccgcccccacctcagcccccacctcagccccctcctcagcccccacctc -cgcccctcctcagcccccacctcagcccccacctcagcccccacctccgccccctcctca -gcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcc -gcccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctca -gcccccacctcagccccctcctcagcccccacctcagcccccacctccgccccctcctca -gcccccacctcccccccacctccgccccctcctcagcccccacctcccccccacctccgc -cccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctcagcc -ccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccc -ccacctcagcccccacctccgcccctcctctgcccccacctcagccccctcctcagcccc -cacctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagccccc -acctcagcccccacctccccccctcctcagcccccacctccacccccacctcagccccca -cctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccac -ctccgcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacc -tcagcccccacctccgcccccacctccgcccccacctcagcccccacctccgccccctcc -tcagcccccacctcagcccccacctcagcccccacctccacccccacctcagcccccacc -tcagcccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctc -aggccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctc -agcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctca -gcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcag -cccccacctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgc -ccctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagcc -cccacctccccccctcctcagcccccacctccacccccacctcagcccccacctccgccc -ctcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgcccc -cacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagccccca -cctccgcccctcctcagcccccacctcagcccccacctccgcccctcctcagcccccacc -tcagcccccacctccacccccacctcagcccccacctcagcccccacctcccccccacct -ccgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctc -agccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctca -gcccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacctca -gcccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgc -ccccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcc -cccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcagccc -ccacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagcccc -cacctccacccccacctcagcccccacctcagcccccacctccgcccctcctcagccccc -acctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccac -ctccgcccccacctcagccccctcctccgcccctcctcagcccccacctccacccccacc -tcagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacct -cagcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacct -cagccccctcctccacccctcctcagcccccacctccgcccccacctcagcccccacctc -cgcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcctcag -cccccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctccgc -ccccacctcagcccccacctccgcccctcctcagcccccacctccacccccacctcagcc -cccacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccc -cacctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccccccct -cctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccac -ctcagcccccacctccacccccacctcagcccccacctcagcccccacctccgcccctcc -tcagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctc -agcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctc -cgcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctca -gaccccacctccgcccccacctccgcccctcctcagcccccacctcagcccccacctcag -cccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctcagcc -cccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagccc -ccacctcagcccccacctccgcccccacctcagccccctcctcagcccccacctcagccc -cctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagccc -cacctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccctc -ctcagcccccacctcagccccctcagcccccacctcagcccccacctccgcccccacctc -cgcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccg -cccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctcagc -cccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctcagcc -cctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcctcagccccc -acctcagcccccacctccgcccccacctccgcccccacctccgcccccacctcagcccct -cctcagcccccacctcagcccccacctcagccccctcctcagcccccacctccgccccca -cctcagcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacc -tccgcccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacct -cagccccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctc -agcccctcctcagcccccacctcagcccctcctcagccccctcctcagcccccacctcag -cccccacctcagcccccacctccgcccccacctccgcccccacctcagccccctcctcag -ccccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgc -ccccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagct -gctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccg -ccacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggc -gccttgt ->p:HG002_2_chr20:63167286-63167728 -gaatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagtt -gctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacgg -ttcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacct -cagtgcccacctcagccccctcctcagcccccacctccgcccccacctcagcccct---- ---------------------cctcagcccccacctcagccccctcctcagcccccacctc -c-----------------------gcccccacctccgcccccacctctgcccct------ --------cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctcc -gcccccacctctgcccct-------------------------------------cctca -gcccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctct -gcccctcctcagcccccacctcagccccctcctcag-----------cccccacctccgc -cccctcctcagcccccacctctgcccct------------cctcagcccccacctcagcc -ccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgccc -ccacctcagcccccacctcc-----------------------gccccctcctcagcccc -cacctctgcccctcctcagcccccacctcagcccccacctcagcccccacctc------- ------------------------------------------------------------- ------------------------------ccccctcctcagcccccacctcagcccccac -ctcagccccctcctcagcccccacctcagcccccacctccgcccct------------cc -tcagcccccacctccgcccccacctcagcccccacctcagcccccacctccgcccccacc -tcagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacc -tctgcccctcctcagcccccacctccgccccctcctcagcccccacctctg--------- ----------------------------cccctcctcagcccccacctcagcccccacctc -agcccccacctcc-cccctcctcagcccccacctcagcccccacctcagccccctcctca -gcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcag -cccccacctccgcccctcctcagcccccacctcag------------------------- ------------------------------------------------------------- ----------ccccctcctcagcccccacctccgcccccacctccgcccccacctctgccc -ctcctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgcccc -cacctccgcccctcctccgcccccacctcagcccccacctccgccccct----------- ------------------------cctcagcccccacctctgcccctcctcagcccccacc -tcagcccccacctcagcccccacct-------------------------cccccctcct -cagcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccca---- --------------------------------------------------------cctca -gcccccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctca -gcccccacctcc-----------gcccccacctcagcccccacctctgcccctcctcagc -ccccacctccgccccctcctcagcccccacctctgcccctcctcagcccccacctcagcc -cccacctcagcccccacct-------------------------cccccctcctcagccc -cca-----------------------------------cctcagcccccacctcagcccc -ctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccccc -a-----------------------cctcagcccccacctccgcccctcctccgcccccac -ctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacc -tccgcccccacctcagccccctcctcagcccccacctc---------------------- ----------------ccccctcctccgcccccacctcagcccccacctcagcccccacct -cagcccccacctc----------------------------------------------- ------------------------------------------------------------- -ccccctcctccgcccccacctcagccccca-----------cctcagcccccacctccgc -ccccacctcagcccccacctcc-------------------------------------- ------------------------------------------------------------- ---------cccctcctcagcccccacctcagcccccacctccgccccca----------- -cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccac -ctccgcccccacctcagcccccacctcagcccccacctccgccccca------------- ---------------------------------------------------------cctc -agcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctc -cgcccccacctccgcccccacctcc-----------gcccccacctcagcccccacctca -gcccccacctccgccccca----------------------------------------- ------cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcc -cccacctcagcccctcctcagcccccacctcagcccccacctcagcccccacctcagccc -ct-------------------------cctcagcccccacctcagccccctcctcagccc -cctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagccc -cacctcagcccctcctcagcccccacctcagccc-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------cctcagccccc -acctcagcccccacctccgcccccacctccgcccccacctcc------------------ ------------------------------------------------------------- ------gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacc -tcc--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------acccccacctccgtccccacctccgccccctcctcagccccctcctcag -cccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgc -ccccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagct -gctggaatgggctaccctcaggagttggcaccccacagcctccttcccttcccacctccg -ccacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggc -gccttgt ->ref_chr20:63167286-63167728 -gaatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagtt -gctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcatgg -ttcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacct -cagtgcccacctcagccccctcctcagccccca--------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------cctcagcccccacctccgcccccacctcagcccctcctcagcccccacctccgc -ccccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagct -gctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccg -ccacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggc -gccttgt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_318281ed61b9dd14b913d8b10c952c34.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_318281ed61b9dd14b913d8b10c952c34.msa deleted file mode 100644 index c866122e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_318281ed61b9dd14b913d8b10c952c34.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:44764040-44764313 -atccatttatccatccatccatccatttatccatccatccatccatccatccacccatcc -atccgtccatccatttatccatccatccatccatccatttatgcatccatttatccatcc -atccatccatccatccatccatccatccatttatcc----atccatccatccatccaccc -atccatccatccgtccatccatttatccatccatccatccatccatccatccatccatcc -atttatccatccgtccatttatccatccatccatccacccacccatccatccatccatcc -acttatccatccacccatccatccatccgtccatccattcatccatccatccatcctccc -acaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatataca ->syndip_2_chr20:44764040-44764313 -atccatttatccatccatccatccatttatccatccatccatccatccatccacccatcc -atccgtccatccatttatccatccatccatccatccatttatgcatccatttatccatcc -atccatccatccatccatccatccatccatccatccatttatccatccatccatccatcc -acccatccatccatccgtccatccatttatccatccatccatccatccatccatccatcc -atttatccatccgtccatttatccatccatccatccacccacccatccatccatccatcc -atttatccatccacccatccatccatccgtccatccattcatccatccatccatcctccc -acaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatataca ->p:HG002_1_chr20:44764040-44764313 -atccatttatccatccatccatccatttatccatccatccatccatccatccacccatcc -atccgtccatccatttatccatccatccatccatccatttatgcatccatttatccatcc -atccatccatccatccatccatccatccatccatccatttatccatccatccatccatcc -acccatccatccatccgtccatccatttatccatccatccatccatccatccatccatcc -atttatccatccgtccatttatccatccatccatccacccacccatccatttatccatcc -atccatccatccacccatccatccatccgtccatccattcatccatccatccatcctccc -acaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatataca ->p:HG002_2_chr20:44764040-44764313 -atccatttatccatccatccatccatttatccatccatccatccatccatccacccatcc -atccgtccatccatttatccatccatccatccatccatttatgcatccatttatccatcc -atccatccatccatccatccatccatccatttatcc----atccatccatccatccaccc -atccatccatccgtccatccatttatccatccatccatccatccatccatccatccatcc -atttatccatccgtccatttatccatccatccatccacccacccatccatccatccatcc -acttatccatccacccatccatccatccgtccatccattcatccatccatccatcctccc -acaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatataca ->ref_chr20:44764040-44764313 ------------------------------------------------------------- ------------------------------------------------------------- -------------atccatttatccatccatccatccatttatccatccatccatccatcc -atccacccatccatccgtccatccatttatccatccatccatccatccatttatgcatcc -atttatccatcc--------atccatccatccatccatccatccatccatttatccatcc -atccatccatccacccatccatccatccgtccatccattcatccatccatccatcctccc -acaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatataca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3309323b7a8f49f7d21f616b3f162df2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3309323b7a8f49f7d21f616b3f162df2.msa deleted file mode 100644 index d02c4b68..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3309323b7a8f49f7d21f616b3f162df2.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:64134783-64136486 -agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc -cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg -acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca -cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca -cacgctccctcagttttgtgcgtc------------------------------------ --acacacacgctccctcagttttgtgcg-------------------------------- ------------------------------------------------------------- -----------------------------------------ccacaaacacgcgcactccc -tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaacacacac -gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac -acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc -acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg -tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt -tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct -cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc -ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt -ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca -cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca -aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa -cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt -cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt -gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt -ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag -ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc -tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc -cctcagttttgtgtg---------------------------------tcacaaacacac -acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg -aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggt ->syndip_2_chr20:64134783-64136486 -agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc -cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg -acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca -cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca -cacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcaca -aacacagacgctccctcagttttgcgca-------------------------------- ------------------------------------------------------------- -----------------------------------------tcacaaacacacacgctccc -tcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacac -gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac -acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc -acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg -tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt -tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct -cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc -ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt -ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca -cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca -aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa -cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt -cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt -gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt -ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag -ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc -tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc -cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac -acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg -aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggt ->p:HG002_1_chr20:64134783-64136486 -agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc -cggtgtgtgatgttccccttgaaaaggaagcgtttctgcttctcctctttccggtccttg -acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca -cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca -cacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcaca -aacacagacgctccctcagttttgcgca-------------------------------- ------------------------------------------------------------- -----------------------------------------tcacaaacacacacgctccc -tcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacac -gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac -acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc -acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg -tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt -tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct -cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc -ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt -ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca -cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca -aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa -cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt -cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt -gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt -ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag -ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc -tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc -cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac -acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg -aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggt ->p:HG002_2_chr20:64134783-64136486 -agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc -cggtgtgtgatgttccccttgaaaaggaagcgtttctgcttctcctctttccggtccttg -acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca -cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca -cacgctccctcagttttgtgcgtc------------------------------------ --acacacacgctccctcagttttgtgcg-------------------------------- ------------------------------------------------------------- -----------------------------------------ccacaaacacgcgcactccc -tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaacacacac -gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac -acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc -acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg -tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt -tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct -cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc -ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt -ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca -cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca -aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa -cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt -cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt -gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt -ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag -ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc -tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc -cctcagttttgtgtg---------------------------------tcacaaacacac -acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg -aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggt ->ref_chr20:64134783-64136486 -agcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtccc -cggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtccttg -acagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacaca -cgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaca -cacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcaca -aacacagacgctccctcagttttgcgcatcacaaacacacacgctccctcagttatggac -atcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagtt -atggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccc -tcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacac -gctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaac -acacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttc -acaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttg -tgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagttt -tgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccct -cagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctcc -ctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacatt -ccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacaca -cacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccca -aacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaaa -cacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcgt -cacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagtttt -gcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagtt -ttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctcag -ttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctccc -tcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctc -cctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacacac -acgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggcttg -aagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattta -gccgttattgagggacatcgaggt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_345063161627fed47b80e3d2c995e708.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_345063161627fed47b80e3d2c995e708.msa deleted file mode 100644 index d63e5a0e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_345063161627fed47b80e3d2c995e708.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:49834072-49834579 -aactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgtaata -ttagcttgtctctctctctctctctctctctctctctctctctctctctctc-------- ---tatatatatatatatatatatacacacacacactatgtatatacacacactgtatata -cgcactatatgcactatatatacacacagtatatgtatatacacacactatatatacagt -gtgtatatatatatatactgtgtatatatatatatactg--tatata------------- ------------------------------------------------------------- ---tatatatatatactgtgtatatatatatactgtgtatatatatatatatactgtatat -atacacacacacactatatatatgccatatataatatctggtggccagttgtgtgaaata -cattcattttctctgttgggtagattga ->syndip_2_chr20:49834072-49834579 -aactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgtaata -ttagcttgtctctctctctctctctctctctctctctctctctctctctctctctatata -tatatatatatatatatatatatacacacacacactatgtatatacacacactgtatata -cgcactatatgcactatatatacacacagtatatgtatatacacacactatatatacagt -gtgtatatatatatatactgtgtatatatatatatactgtatatatatatatactgtgta -tatatatatatactgtgtatatatatatactgtgtatatatatatactgtatatatatac -tgtatatatatatatatactgtatatatatatactgtgtatatatatatatactgtatat -atacacacacacactatatatatgccatatataatatctggtggccagttgtgtgaaata -cattcattttctctgttgggtagattga ->p:HG002_1_chr20:49834072-49834579 -aactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgtaata -ttagcttgtctctctctctctctctctctctctctctctctctctctctctctctatata -tatatatatatatatatatatatacacacacacactatgtatatacacacactgtatata -cgcactatatgcactatatatacacacagtatatgtatatacacacactatatatacagt -gtgtatatatatatatactgtgtatatatatatatactgtatatatatatatactgtgta -tatatatatatactgtgtatatatatatactgtgtatatatatatactgtatatatatac -tgtatatatatatatatactgtatatatatatactgtgtatatatatatatactgtatat -atacacacacacactatatatatgccatatataatatctggtggccagttgtgtgaaata -cattcattttctctgttgggtagattga ->p:HG002_2_chr20:49834072-49834579 -aactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgtaata -ttagcttgtctctctctctctctctctctctctctctctctctctctctctc-------- ---tatatatatatatatatatatacacacacacactatgtatatacacacactgtatata -cgcactatatgcactatatatacacacagtatatgtatatacacacactatatatacagt -gtgtatatatatatatactgtgtatatatatatatactgtatatata------------- ------------------------------------------------------------- ---tatatatatatatatactgtatatatatatactgtgtatatatatatatactgtatat -atacacacacacactatatatatgccatatataatatctggtggccagttgtgtgaaata -cattcattttctctgttgggtagattga ->ref_chr20:49834072-49834579 -aactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgtaata -ttagcttgtctctctctctctctctctctctctctctctctctctctctctctctatata -tatatatatatatatatatatatacacacacacactatgtatatacacacactgtatata -cgcactatatgcactatatatacacacagtatatgtatatacacacactatatatacagt -gtgtatatatatatatactgtgtatatatatatatactgtatatatatatatactgtgta -tatatatatatactgtgtatatatatatactgtgtatatatatatactgtatatatatac -tgtatatatatatatatactgtatatatatatactgtgtatatatatatatactgtatat -atacacacacacactatatatatgccatatataatatctggtggccagttgtgtgaaata -cattcattttctctgttgggtagattga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_351515eae575f51a5c58a89edbda4b09.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_351515eae575f51a5c58a89edbda4b09.msa deleted file mode 100644 index 9e58793b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_351515eae575f51a5c58a89edbda4b09.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:16395049-16395521 -acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt -gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa -ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag -gaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggc -caagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga -gaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggaggg -gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggagaa -gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc -atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaa ->syndip_2_chr20:16395049-16395521 -acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt -gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaaa -ggagatgaggaaggggagaggaggggagaggaggggag---------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------gggaggggaggggagaggaggggaggccaagggagaa -gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc -atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaa ->p:HG002_1_chr20:16395049-16395521 -acagtcatggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcattggt -gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaaa -ggagatgaggaaggggagaggaggggagaggaggggag---------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------gggaggggaggggagaggaggggaggccaagggagaa -gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc -atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaa ->p:HG002_2_chr20:16395049-16395521 -acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt -gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa -ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag -gaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggc -caagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga -gaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggaggg -gaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggagaa -gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc -atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaa ->ref_chr20:16395049-16395521 -acagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcggt -gtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaaa -ggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggagag -gaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggc -caa-----gggaggggaggggaggagaggggaggccaagggaggggaggggaggggagga -gaggggaggccaa----------------------------------------------- ------------------------gggaggggaggggaggagaggggaggccaagggagaa -gatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttcctttc -atataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggcttttg -gtattcaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_373e1d1ae04c109544621b85b6e2768d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_373e1d1ae04c109544621b85b6e2768d.msa deleted file mode 100644 index ed703593..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_373e1d1ae04c109544621b85b6e2768d.msa +++ /dev/null @@ -1,105 +0,0 @@ ->syndip_1_chr20:62320931-62321973 -aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc -agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca -gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga -aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg -tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg -cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg -gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggaagag -gtggggccagtgggggtggggtcagtggaggggtggggtcagaggacaggtgggttcaga -ggacgggtgggttcagaggacgggtgggttcagaggacgggtggggtcagtggaggggtg -gggtcagtggaggggtagggtcagaggacgggtagggtcagtggaggggtagggccagca -gaggggtggggtcagcggaggggtggggtcagtggaggggtggggtcagtggaggggtgg -ggtcagtggaggcagggtcagtgaaagggtggcgccagtggaggaagagggcgccagtgg -aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg -gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg -aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg -gccagcagaggggtggggccagt-----------------ggaggggtggggccagcgga -ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga -aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt -tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttgga ->syndip_2_chr20:62320931-62321973 -aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc -agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca -gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga -aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg -tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg -cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg -gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggcagag -gtggggccagtgggggtggggtcagtggaggggtggggtcagaggac------------- ------------------------------------------------------------- -----------------------------------------------gggtagggtcagtg -gaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggaggggtgg -ggtcagtggaggcagggtcagtgaaagggt-------------------ggcgccagtgg -aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg -gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg -aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg -gccagcagaggggtggggccagtggaggggtggggccagcggaggggtggggccagcgga -ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga -aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt -tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttgga ->p:HG002_1_chr20:62320931-62321973 -aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc -agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca -gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga -aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg -tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg -cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg -gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggcagag -gtggggccagtgggggtggggtcagtggaggggtggggtcagaggac------------- ------------------------------------------------------------- -----------------------------------------------gggtagggtcagtg -gaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggaggggtgg -ggtcagtggaggcagggtcagtgaaagggt-------------------ggcgccagtgg -aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg -gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg -aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg -gccagcagaggggtggggccagtggaggggtggggccagcggaggggtggggccagcgga -ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga -aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt -tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttgga ->p:HG002_2_chr20:62320931-62321973 -aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc -agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca -gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga -aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg -tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg -cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg -gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggaagag -gtggggccagtgggggtggggtcagtggaggggtggggtcagaggacaggtgggttcaga -ggacgggtgggttcagaggacgggtgggttcagaggacgggtggggtcagtggaggggtg -gggtcagtggaggggtagggtcagaggacgggtagggtcagtggaggggtagggccagca -gaggggtggggtcagcggaggggtggggtcagtggaggggtggggtcagtggaggggtgg -ggtcagtggaggcagggtcagtgaaagggtggcgccagtggaggaagagggcgccagtgg -aggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg -gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg -aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg -gccagcagaggggtggggccagt-----------------ggaggggtggggccagcgga -ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga -aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt -tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttgga ->ref_chr20:62320931-62321973 -aggccaggggagaatgatcagctggggccctggggtcattagggtggggagggctcagcc -agaggtcatgaggtcagcttagggacacaggacctgtggggaggtcccagagttctggca -gagtcatagggtcaggtaggagtcagatgggagtgaagggcatggggtcacccagggaga -aggtagggccagcacaaggggttggggccggaggtggggccagtgaaggggcggggccgg -tggaggcagggtcagtgaaggggtggggccagtggaggaagagggggccagtggaggagg -cggggcctgtggaggggtggggccagtggaggcagggtcagtgaaggggtggggccggtg -gaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtggaagag -gtggggccagtgggggtggggtcagtggaggggtggggtcagaggacgggtgggt----- ------------------------------------------------------------- ---------------------tcagaggacgggtagggtcagtggaggggtagggccagca -gaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggaggggtgg -ggtcagtggaggcagggtcagtgaaagggt------------------------------ ---------ggcgccagtggaggaagagggggccagtggaggcagggcctgtggaggggtg -gggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagccagtgg -aagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggaggcagg -gccagcagaggggtggggtcagt-----------------ggaggggtggggccagtgga -ggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcacacagga -aggctagggacagtagaggggtgcagccagcagtggagctgcagcgctcctcagcgtggt -tggagttggacaggcatgggtctctcgggaaatggaaggcagctgggaccactctgggag -gtcgacgttaacactggggtcaccaggctgtgtgggacttgga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_376668b7c494376b87a6d62816059791.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_376668b7c494376b87a6d62816059791.msa deleted file mode 100644 index 6df96a24..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_376668b7c494376b87a6d62816059791.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:41196260-41196605 -aggggtatatatatatataatatatataaataaatatataaaaataaatatatatttata -ataaatatatttttatttcatatataaatatatatcttataaatatatatatttatataa -cataaatatatatttatatatattata------------------------aatatatat -tatatataatatatatttatataaatatatatattatatataatatatttatatataata -tatatttatatattataaatatatattatatataatatatatttatataaatatatatta -tatataaatatatattatatataatatatatttatataaatatatattatatattatata -aatattatatataatatatattta-----tataaatatatattatatattataaatatat -attatatattatatattatataaatattatatataatatatattatatataatatatata -aaaatatatatatttatatatataaatatttt ->syndip_2_chr20:41196260-41196605 -aggggtatatatatatataatatatataaataaatatataaaaataaatatatatttata -ataaatatatttttatttcatatataaatatatatcttataaatatatatatttatataa -cataaatatatatttatatatattatataacataaatatatatttatatatattatatat -tatatataatatatatttatataaatatatatattatatataatatatttatatataata -tatatttatatattataaatatatattatatataatatatatttatataaatatatatta -tatat-----------------------------tataaatatatattatatattatata -aatattatatataatatatattta-----tataaatatataatatatattataaatatat -attatatattatatattatataaatattatatataatatatattatatataatatatata -aaaatatatatatttatatatataaatatttt ->p:HG002_1_chr20:41196260-41196605 -aggggtatatatatatataatatatataaataaatatataaaaataaatatatatttata -ataaatatatttttatttcatatataaatatatatcttataaatatatatatttatataa -cataaatatatatttatatatattatatattatatatatatatttatatatattatatat -tatatataatatatatttatataaatatatatattatatataatatatttatatataata -tatatttatatattataaatatatattatatataatatatatttatataaatatatattt -atata-----------------------------aatatatatattatatataatatat- -----ttatatataatatatatttatatattataaatatatattatatattataaatatat -attatatattatatattatataaatattatatataatatatattatatataatatatata -aaaatatatatatttatatatataaatatttt ->p:HG002_2_chr20:41196260-41196605 -aggggtatatatatatataatatatataaataaatatataaaaataaatatatatttata -ataaatatatttttatttcatatataaatatatatcttataaatatatatatttatataa -cataaatatatatttatatatattata------------------------aatatatat -tatatataatatatatttatataaatatatatattatatataatatatttatatataata -tatatttatatattataaatatatattatatataatatatatttatataaatatatatta -tatataaatatatattatatataatatatatttatataaatatatattatatattatata -aatattatatataatatatattta-----tataaatatatattatatattataaatatat -attatatattatatattatataaatattatatataatatatattatatataatatatata -aaaatatatatatttatatatataaatatttt ->ref_chr20:41196260-41196605 -aggggtatatatatatataatatatataaataaatatataaaaataaatatatatttata -ataaatatatttttatttcatatataaatatatatcttataaatatatatatttatataa -cataaatatatatttatatatat------------------------------tatatat -tatatataatatatatttatataaatatatatattatatataatatatttatatataata -tatatttatatat----------------------------------------------- ------------------------------------------------------------- ------------------------------tataaatatatattatatattataaatatat -attatatattatatattatataaatattatatataatatatattatatataatatatata -aaaatatatatatttatatatataaatatttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_37addba43ca0bef896cc3f8296ac4789.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_37addba43ca0bef896cc3f8296ac4789.msa deleted file mode 100644 index 9d06ac16..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_37addba43ca0bef896cc3f8296ac4789.msa +++ /dev/null @@ -1,345 +0,0 @@ ->syndip_1_chr20:64131704-64134055 -aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc -acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc -tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag -accccctcactgtcaactctcatgtcctatagagaccccctcactgtcaactctcatgtc -ctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccc -tcatgtcctata--------------------------------gagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatg -agaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccactctcatg -tcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatagaga -ccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcct -atagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccct -catgtcctatgagaccccctcactgtccactctcatgtcctat-gagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctata -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatg -tcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccac -cctcatgtcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagac -cccctcactgtccaccctcatgt------------------------------------- ------------------------------------------------------------- -----cctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagacccc -ctcactgtccactctcatgtcctatagagacccctcactgtccaccctcatggcctatag -agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtg -tcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac -tctcatgtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcac -tgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagagacc -ccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcatggc---------------------- ------------------------------------------------------------- ----------------------------------------------------ctgtagaga -ccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctat----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctc -actgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctatagag -accccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctatagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactctccaccctcatgtcctat -agagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctca -tgtcctat-gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtc -caccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatag -agaccccctcactctccaccctcatggcctatagagaccccctcactgtccaccctcgtg -tcctatagagaccccctcactctccaccctcatggcctatagagaccccctcactgtcca -ccctcatggcctatagagaccccctcactgtccactctcatgtcctatgagaccccctca -ctgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatgagac -cccctcactgtccactctcatgtcctat-gagaccccctcactgtccaccctcatggcct -gtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctc -gtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccactctcatgtcctatgagaccccct -cactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatggcctatagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccactctcatggcctgtagagaccccctcact -gtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt -gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc ->syndip_2_chr20:64131704-64134055 -aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc -acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc -tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag -accccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggc -ctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagacccctcactgtccaccctcatggcctatgagaccccctcactgt -ccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacccc -ctcactgtccaccctcatgtcctatagaga-cccctcactgtccaccctcatggcctatg -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccctca -ctgtccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagaga -ccccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctcgtgtcct -atagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccct -catgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcgtgtccta---------------------------- ------------------------------------------------------------- -------------tagagaccccctcactgtccaccctcatggcctatagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagac -cccctcactgtccaccctcatgg------------------------------------- ------------------------------------------------------------- -----cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctat------------------------------------------- ------------------------------------------------------------g -agaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgtg -tcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac -cctcatgtcctata---------------------------------------------- ---------------------gagaccccctcactgtccaccctcatggcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggccta -tagagaccccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctca -tggcctatagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtcc -accctcgtgtcctatgagaccccctcactgtccaccctcatggcctatagagaccccctc -actgtccaccctcatggcctatgagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc -tcatgtcctatgagaccccctcactgtccactctcatgtcctatagagacccctcactgt -ccaccctcatggcctatagagaccccctcactgtccaccctcatggcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatggcctata---------- ------------------------------------------------------------- -------------------------------gagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccc -tcatggcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgtgtcctat -agagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcatggcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatag -agaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtcca -ccctcatggcctatagagaccccctcactgtccaccctcatggcctatgagaccccctca -ctgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagaga -cccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcct -atagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata--------- ------------------------------------------------------------- -------------------------------gagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcgtgtcctatagagaccccctcactgtccacccatatggcctgtagagaccccctcact -gtccaccctcatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt -gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc ->p:HG002_1_chr20:64131704-64134055 -aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc -acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc -tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag -accccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatggc -ctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagacccctcactgtccaccctcatggcctatgagaccccctcactgt -ccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacccc -ctcactgtccaccctcatgtcctatagaga-cccctcactgtccaccctcatggcctatg -agaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccctca -ctgtccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagaga -ccccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctcgtgtcct -atagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccct -catgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcgtgtccta---------------------------- ------------------------------------------------------------- -------------tagagaccccctcactgtccaccctcatggcctatagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagac -cccctcactgtccaccctcatgg------------------------------------- ------------------------------------------------------------- -----cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatgtcctat------------------------------------------- ------------------------------------------------------------g -agaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgtg -tcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac -cctcatgtcctata---------------------------------------------- ---------------------gagaccccctcactgtccaccctcatggcctatagagacc -ccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggccta -tagagaccccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctca -tggcctatagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtcc -accctcgtgtcctatgagaccccctcactgtccaccctcatggcctatagagaccccctc -actgtccaccctcatggcctatgagaccccctcactgtccaccctcatggcctgtagaga -ccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc -tcatgtcctatgagaccccctcactgtccactctcatgtcctatagagacccctcactgt -ccaccctcatggcctatagagaccccctcactgtccaccctcatggcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatggcctata---------- ------------------------------------------------------------- -------------------------------gagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccc -tcatggcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgtgtcctat -agagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtc -caccctcatggcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatag -agaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatg -tcctatagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtcca -ccctcatggcctatagagaccccctcactgtccaccctcatggcctatgagaccccctca -ctgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagaga -cccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcct -atagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata--------- ------------------------------------------------------------- -------------------------------gagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcgtgtcctatagagaccccctcactgtccacccatatggcctgtagagaccccctcact -gtccaccctcatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt -gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc ->p:HG002_2_chr20:64131704-64134055 -aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc -acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc -tcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagag -accccctcactgtcaactctcatgtcctatagagaccccctcactgtcaactctcatgtc -ctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccaccc -tcatgtcctata--------------------------------gagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatg -agaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccactctcatg -tcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac -cctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatagaga -ccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcct -atagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccct -catgtcctatgagaccccctcactgtccactctcatgtcctat-gagaccccctcactgt -ccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctata -gagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcatg -tcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccac -cctcatgtcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagac -cccctcactgtccaccctcatgt------------------------------------- ------------------------------------------------------------- -----cctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagacccc -ctcactgtccactctcatgtcctatagagacccctcactgtccaccctcatggcctatag -agaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtg -tcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccac -tctcatgtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcac -tgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagagacc -ccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcatggc---------------------- ------------------------------------------------------------- ----------------------------------------------------ctgtagaga -ccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctat----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctc -actgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctatagag -accccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctatagagaccc -cctcactgtccaccctcgtgtcctatagagaccccctcactctccaccctcatgtcctat -agagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctca -tgtcctat-gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtc -caccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagaccccc -tcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatag -agaccccctcactctccaccctcatggcctatagagaccccctcactgtccaccctcgtg -tcctatagagaccccctcactctccaccctcatggcctatagagaccccctcactgtcca -ccctcatggcctatagagaccccctcactgtccactctcatgtcctatgagaccccctca -ctgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatgagac -cccctcactgtccactctcatgtcctat-gagaccccctcactgtccaccctcatggcct -gtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctc -gtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccactctcatgtcctatgagaccccct -cactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatggcctatagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatagagaccccctcactgtccactctcatggcctgtagagaccccctcact -gtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt -gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc ->ref_chr20:64131704-64134055 -aggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactcc -acactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagacttc -tcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagag -accccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatggc -ctgta------------------------------------------------------- ---------------------------------------------gagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagacccc -ctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatg -agaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatg -tcctata----------------------------------------------------- -------------------------------------------------gagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagaga -ccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgt--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------cctatagagaccccctca -ctgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagac -cccctcactgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcct -atagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtccactctc -atggcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcactgt -ccaccctcatggcctgt------------------------------------------- -----------------------------------------------------------ag -agaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatg -gcctgtagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtccac -cctcatgtcctat----------------------------------------------- ---------------------gagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtccta -tagagaccccctcactgtccgccctcatgtcctatgagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcatggc---------------------- ------------------------------------------------------------- ----------------------------------------------------ctgtagaga -ccccctcactgtccgccctcatgtcctat------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------gagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtcc -accctcatgtcctatagagaccccctcactgtccaccctcatgtcctat----------- ------------------------------------------------------------- -------------------------------gagaccccctcactgtccaccctcatgtcc -tat-gagaccccctcactgtccaccctcatgtcctatgaga------------------- ------------------cccctcactgtccaccctcatgtcctatgagaccccctcactg -tccaccctcatgtcctat------------------------------------------ ------------------------------------------------------------- ------------------------------------gagaccccctcactgtccactctca -tgtcctat-gaga-cccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatggcctgtagagaccccctcactgtcaactctcatgtcctat-gagaccccc -tcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc----- -------------------------------aaagagaccccctcactgtccaccctcatg -gcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcca -ccctcatggcctatagagaccccctcactgtccaccctcatgtccaaagagaccccctca -ctgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgta---- ------------------------------gagaccccctcactgtccaccctcatgtcct -atagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccctc -atggcctgta---------------------------------gagaccccctcactgtc -cacccatatggcctgtagagaccccctcactgtccaccctcatgtcctata--------- ------------------------------------------------------------- -------------------------------gagaccccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc -tcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcact -gtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcattt -gctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaagggc -cctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_37dc1e3da979ee027d03cd84019b4904.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_37dc1e3da979ee027d03cd84019b4904.msa deleted file mode 100644 index ec43eebc..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_37dc1e3da979ee027d03cd84019b4904.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:13848064-13848749 -tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag -aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg -cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag -agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga -gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag -aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa -gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg -aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag -aagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaag -aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga -caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac -tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaat ->syndip_2_chr20:13848064-13848749 -tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag -aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg -cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag -agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga -gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag -aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa -gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg -aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag -aagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaag -aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga -caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac -tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaat ->p:HG002_1_chr20:13848064-13848749 -tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag -aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg -cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag -agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga -gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag -aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa -gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg -aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag -aagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaag -aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga -caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac -tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaat ->p:HG002_2_chr20:13848064-13848749 -tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag -aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg -cgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaag -agagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagga -gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaag -aagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa -gtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggagg -aagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaag -aagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaag -aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaaga -caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac -tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaat ->ref_chr20:13848064-13848749 -tctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggcag -aggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaattg -cgtctcaaaaaaaaaaaagaagaagaaaagtagaagacgaagatgaagaagaataagaag -agagaaaagaagaagagaaggttagagaaaagaagagaa--------------------- -----gagaaggagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaa -gaagaagaagaagaagaagtcaaatatctgg---agaagaagaagaagaggaagaagaag -aaaaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaagaa -gtcaaatatctggagaagaagaagaagaagaggaagaagaagaagaagaggaggaggaag -aaggagaaggagaaggagaaggagaagga------------------------------- ------------------------------------------gaaggagaaggagaagaag -aagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaaata -caaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttacac -tctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcca -gagaat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_39f32e213738999402fb2b5bda16e98a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_39f32e213738999402fb2b5bda16e98a.msa deleted file mode 100644 index f1407a9e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_39f32e213738999402fb2b5bda16e98a.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:61561999-61562362 -gaccccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggct -cccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagagg -gacttccgtgtggagaggtggaccccagggctcccggagagagagagggacctccctgag -agagagagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggac -ctccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggag -aggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtggacccca -gggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccg--g -agagagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacct -ctgtgtggagaggtggaccccagggctcccggagagagagagggacctc ->syndip_2_chr20:61561999-61562362 -gaccccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggct -cccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagagg -gacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctccc---- ------------------tgtggagaggtggaccccagggctcccagagagagagagggac -cttcgtgtggagaggtggaccccagggctccc--ggagagagagggacctccgtgtggag -aggtggaccccagggctcccggagagagagagggacctctgtgtggagaggtggacccca -gggctcccggagagagagagggacctc--------------------------------- ------------------------------------------------------------- -------------------------------------------------- ->p:HG002_1_chr20:61561999-61562362 -gaccccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggct -cccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagagg -gacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctccc---- ------------------tgtggagaggtggaccccagggctcccagagagagagagggac -cttcgtgtggagaggtggaccccagggctccc--ggagagagagggacctccgtgtggag -aggtggaccccagggctcccggagagagagagggacctctgtgtggagaggtggacccca -gggctcccggagagagagagggacctc--------------------------------- ------------------------------------------------------------- -------------------------------------------------- ->p:HG002_2_chr20:61561999-61562362 -gaccccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggct -cccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagagg -gacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctccctgag -agagagagggacctccctgtggagaggtggaccccagggctcccggagagagagagggac -ctccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggag -aggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtggacccca -gggctcccagagagagagagggaccttcgtgtggagaggtggaccccagggctcccggag -agagagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacct -ctgtgtggagaggtggaccccagggctcccggagagagagagggacctc ->ref_chr20:61561999-61562362 -gaccccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggct -cccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagagg -gacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctccc---- ------------------tgtggagaggtggaccccagggctcccagagagagagagggac -cttcgtgtggagaggtggaccccagggctccc--ggagagagagggacctccgtgtggag -aggtggaccccagggctcccggagagagagagggacctctgtgtggagaggtggacccca -gggctcccggagagagagagggacctc--------------------------------- ------------------------------------------------------------- -------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3a3d4bda444ca93397f3574b58e71451.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3a3d4bda444ca93397f3574b58e71451.msa deleted file mode 100644 index 681ffc5d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3a3d4bda444ca93397f3574b58e71451.msa +++ /dev/null @@ -1,100 +0,0 @@ ->syndip_1_chr20:57090572-57091511 -agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt -aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg -ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc -accaccacacactccaccatgcacacacacctccacgcacacacacctccacccgcacac -acacacaccttcaccaccacacactccacccacacacacctccacccacacacctcca-- ---------------cccacacacacctccgcccacacacacctccgcccacacacacctc -cacccacacacacctccacccacacacctccgcccacacacacctccgccctcacacacc -tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca -cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc -acccacacacacctccacccacacgccacccatgcacacacctccacccacacacacaca -caccacccacccacacacacctccacccgcacacacctccaccaccacacacacctccac -ccacacacaccacccatgcacacacctccacccacacacacacacacctccacccacaca -cacctccacccacacacacctccacccacacacacacacctccacccacccacacacacc -tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc -acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc -tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc -tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg -attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaagga ->syndip_2_chr20:57090572-57091511 -agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt -aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg -ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc -accaccacacactccgccatgcacacacacctccacgcacacacacctccacccgcacac -acacacaccttcaccaccacacactccacccacacacacctccacccacacacctccacc -cacacacacctccgcccacacacacctccgcccacacacacctccgcccacacacacctc -cacccacacacacctccgcccacacacctccgcccacacacacctccgccctcacacacc -tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca -cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc -acccacacaca-----------------------cacacacctccacccacacaca---- ---------------------------------------------------------ccac -ccacacacaccacccatgcacacacctccacccaca------------------------ ---------------------------------------------------cacacacacc -tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc -acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc -tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc -tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg -attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaagga ->p:HG002_1_chr20:57090572-57091511 -agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt -aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg -ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc -accaccacacactccgccatgcacacacacctccacgcacacacacctccacccgcacac -acacacaccttcaccaccacacactccacccacacacacctccacccacacacctccacc -cacacacacctccgcccacacacacctccgcccacacacacctccgcccacacacacctc -cacccacacacacctccgcccacacacctccgcccacacacacctccgccctcacacacc -tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca -cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc -acccacacaca-----------------------cacacacctccacccacacaca---- ---------------------------------------------------------ccac -ccacacacaccacccatgcacacacctccacccaca------------------------ ---------------------------------------------------cacacacacc -tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc -acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc -tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc -tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg -attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaagga ->p:HG002_2_chr20:57090572-57091511 -agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt -aagccacgaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg -ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc -accaccacacactccaccatgcacacacacctccacgcacacacacctccacccgcacac -acacacaccttcaccaccacacactccacccacacacacctccacccacacacctcca-- ---------------cccacacacacctccgcccacacacacctccgcccacacacacctc -cacccacacacacctccacccacacacctccgcccacacacacctccgccctcacacacc -tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca -cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc -acccacacacacctccacccacacgccacccatgcacacacctccacccacacacacaca -caccacccacccacacacacctccacccgcacacacctccaccaccacacacacctccac -ccacacacaccacccatgcacacacctccacccacacacacacacacctccacccacaca -cacctccacccacacacacctccacccacacacacacacctccacccacccacacacacc -tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc -acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc -tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc -tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg -attactgggtcctgccggtctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaagga ->ref_chr20:57090572-57091511 -agcacagtgaggcccacttcagacttccgagctccagactatgagatcaagtgttgtttt -aagccaccaagtttgggaaaatttgccacagcagcaagaggaaacgaacgcactcaggtg -ctcctgccacacacactcacagttgcacaagctggtgcagctccagacccacacacctcc -accaccacacactccgccatgcacacacacctccacgcacacacacctccacccgcacac -acacacaccttcaccaccacacactccacccacacacacctccacccacacacctccacc -cacacacacctccgcccacacacacctccgcccacacacacctccgcccacacacacctc -cacccacacacacctccgcccacacacctccgcccacacacacctccgccctcacacacc -tccacccacacacacctccacccacacacgcctccacccgcacacacctccaccaccaca -cacacctccacccacacacaccacccatgcacacacctccacccacacacacacacctcc -acccacacaca-----------------------cacacacctccacccacacaca---- ---------------------------------------------------------ccac -ccacacacaccacccatgcacacacctccacccaca------------------------ ---------------------------------------------------cacacacacc -tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc -acacctccactggcacacaccacccatgcacacacctccactggcacgcactactccacc -tgcgtgcgcctcccacctgcgttcaccctccacctgtgttcgctcccacccactcatgcc -tctccacccgcaaaagtgtgagtgctgaggctgggactcaacctgagccgctggctctgg -attactgggtcctgccgggctggccaggcctggtcacaggccgggtcccagtcagcagct -ctttacctcaacaagga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3ba0420a0f6db81c0d76f7ba53ba5226.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3ba0420a0f6db81c0d76f7ba53ba5226.msa deleted file mode 100644 index b000d0b7..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3ba0420a0f6db81c0d76f7ba53ba5226.msa +++ /dev/null @@ -1,180 +0,0 @@ ->syndip_1_chr20:59383704-59385335 -ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc -aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc -tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg -ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa -ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg -gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg -aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga -ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga -tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag -taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag -ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg -ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg -gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg -tgagca------------------------------------------------------ --------gggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga -ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga -ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg -aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt -gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt -ggggaagtggtgagaggggaggaggtgagggggcaagggaggtgatgcggaggaaggagg -tgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggt -gatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtg -atgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtga -tgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgat -gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg -ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg -gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg -aaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggga -aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa -ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag -gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg -aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg -aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt -taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatggg ->syndip_2_chr20:59383704-59385335 -ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc -aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc -tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg -ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa -ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg -gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg -aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga -ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga -tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag -taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag -ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg -ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg -gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg -tgagcagggaggaggtgagggggcaagggaggtgatggggaggaggtgagtggggaggtg -gtgagcggggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga -ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga -ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg -aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt -gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt -ggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcgga--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------ggaaggaggtgat -gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg -ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg -gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg -gaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatggga -aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa -ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag -gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg -aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg -aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt -taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatggg ->p:HG002_1_chr20:59383704-59385335 -ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc -aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc -tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg -ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa -ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg -gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg -aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga -ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga -tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag -taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag -ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg -ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg -gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg -tgagcagggaggaggtgagggggcaagggaggtgatggggaggaggtgagtggggaggtg -gtgagcggggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga -ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga -ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg -aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt -gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt -ggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcgga--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------ggaaggaggtgat -gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg -ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg -gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg -gaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatggga -aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa -ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag -gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg -aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg -aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt -taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatggg ->p:HG002_2_chr20:59383704-59385335 -ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc -aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc -tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg -ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa -ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg -gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg -aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga -ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggggggaaggaagtga -tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag -taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag -ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg -ggaaggaggtgatggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggg -gaggatgtgggggaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtgg -tgagca------------------------------------------------------ --------gggaggaggtgagggggcaagggaggtgatggggaggaaggaggttatgggga -ggtggtgagtggggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtgggga -ggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgggg -aggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggaggt -gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt -ggggaagtggtgagaggggaggaggtgagggggcaagggaggtgatgcggaggaaggagg -tgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggt -gatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtg -atgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtga -tgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgat -gggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaaggaggtgatg -ggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg -gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg -aaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggga -aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggaa -ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag -gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg -aggtgagaggggaggagctgaggggggaaggaggtaatgaggacaaggtgaggggaaagg -aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt -taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatggg ->ref_chr20:59383704-59385335 -ggttttgtgcttccaccaagccaggggactgttctgtggccctggaaccaccgtgaaagc -aaacaaccctcggctgtgttgggagacagctccagctcctccatcctcaaatgtgagagc -tgatgattggggtggaggaggaggtgagtggggagggggtgggggagaaggaggtgatgg -ggaagagatgagtgggcaggaggtgagcagggaggaggtgagcagggatgagtggaggaa -ggaggtgatagggaggaggtgagtgggcaggaggtgagcagggagaagatgagcaggggg -gtggtgagcggggaggaggtggaggggaaggaagtgatgggggaggaggtggggggaagg -aggtgatggggaggaggtgaatgggcaggaggtgactggggaggaggtgagcagggagga -ggtgagcagggaggaggtgagtggagtggggatgggagtggagtggcgggaaggaagtga -tagggaggagatgagtgggcaggaggtgagcagagaggagatgagtagagcagggatgag -taggggaaggaggtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcag -ggaggaggtagaggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcggg -ggaa-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------ggaggtgatggggaggaggtgagtgggg -aggaaggtggggggaaggaggtgatagggaggatgtgggggaggtgggggggaaggaggt -gaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtgagt -ggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcgga--------- ------------------------------------------------------------- --------------------------------------------------ggaaggaggtg -atgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtga -tggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgat -ggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatg -gggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgg -gaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggg -gaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggg -aggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatgggga -ggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggag -gaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggagg -aggtgagaggggaggagctgagtggggaaggaggtaatgaggacaaggtgaggggaaagg -aggtaagggaggggaaggggagggaaggagctgagcggggcagagcatgtctcctctctt -taagcatcctctgtattctgcagaggccaagcagtctggatgttggccttcctcagtggc -ccatgaaataactttgctccccagattctgagcatggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_3d73cc7182161a9c5e90b812c17b9c4a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_3d73cc7182161a9c5e90b812c17b9c4a.msa deleted file mode 100644 index 55858c55..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_3d73cc7182161a9c5e90b812c17b9c4a.msa +++ /dev/null @@ -1,100 +0,0 @@ ->syndip_1_chr20:278800-279286 -gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa -tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------gggcg -gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggagg -gagggcgggagggagggacggagggaggaagggcgggacggagggagggagggcgggagg -gacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagg -gcgggagggcgggacggagggagggag---ggagggagggcgggacggagggagggaggg -agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga -gggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggga -gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga -gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca -gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacgg ->syndip_2_chr20:278800-279286 -gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa -tgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggcg -cgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggagg -gagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcgg -gacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcgg -gacggagggagggagggagggagggcgggacggagggagggagggcgggacggagggagg -gagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgg -gacggagggcgggagggcgggacggagggagggagggcgggacggagggacggagggagg -gagggcgggacggagggagggagggcgggacggagggacggagggagggagggcgggacg -gagggagggagggagggacggagggcgggacggcgggagggcgggacggagggacggagg -gagggcgggacggagggcgggagggagggagggcgggacggagggagggagggagggagg -gcgggacggagggagggagggagggagggacggagggacggagggagggagggagggagg -gacggagggcgggacggagggagggagggcggagggagggagggcgggacggagggaggg -agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga -gggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggga -gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga -gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca -gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacgg ->p:HG002_1_chr20:278800-279286 -gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa -tgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggcg -cgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggagg -gagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcgg -gacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcgg -gacggagggagggagggagggagggcgggacggagggagggagggcgggacggagggagg -gagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgg -gacggagggcgggagggcgggacggagggagggagggcgggacggagggacggagggagg -gagggcgggacggagggagggagggcgggacggagggacggagggagggagggcgggacg -gagggagggagggagggacggagggcgggacggcgggagggcgggacggagggacggagg -gagggcgggacggagggcgggagggagggagggcgggacggagggagggagggagggagg -gcgggacggagggagggagggagggagggacggagggacggagggagggagggagggagg -gacggagggcgggacggagggagggagggcggagggagggagggcgggacggagggaggg -agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga -gggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggga -gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga -gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca -gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacgg ->p:HG002_2_chr20:278800-279286 -gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa -tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------gggcg -gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggagg -gagggcgggagggagggacggagggaggaagggcgggacggagggagggagggcgggagg -gacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagg -gcgggagggcgggacggagggagggag---ggagggagggcgggacggagggagggaggg -agggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgga -gggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggga -gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga -gggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagca -gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacgg ->ref_chr20:278800-279286 -gatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaaa -tgcgtcttccaggtggaggaagcaccacgtgcagt------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------gggcg -gggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggagg -gagggcg--------------------------------ggacggagggagggagggagg -gacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagg -gcgggagggcgggacggag----------------------------------------- ------------------------------------------------------------- ------------------------------------------ggaggga----gggaggga -gggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgga -gggacggagggcgggcggatgccgcgggtctcaccgccagggtgtcctgctgctgcagca -gggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctccc -ggttgagcttgctgaggaagttctcacgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_405fa3f356dead7f68ddb49001c0e603.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_405fa3f356dead7f68ddb49001c0e603.msa deleted file mode 100644 index 22915bfb..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_405fa3f356dead7f68ddb49001c0e603.msa +++ /dev/null @@ -1,105 +0,0 @@ ->syndip_1_chr20:20295855-20296665 -gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc -agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca -acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt -cttcctccctcccttcct---tcccttccttcccttccttccctcctttt--cttccttc -tttccttccttccttccctccctccttcccttccttccttccttcc-cttccttccttct -ctccttccttccttccctccctccttcccttccttccttctctccttccttcccttcctt -ccttctctccttccttcccttccttccttctctccttccttcccttccttccttctctcc -ttccttcccttccttccttctctccttccttcccttgcttcctttcttccttcctttgct -tccttgcttccttctttcctttcttcatccctccctccctccttccttcctttccttcct -tccctctatccttccttccttcctttctttctccctcccttccttcccttccttccttcc -ctcttttccttccatctttcctttcttcctccctccctccctccttccctccttcattac -ttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttcct -tcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatccc -ttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgctt -ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc -tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc -ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc -ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt -taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca -gatagtcaaataactgtaa ->syndip_2_chr20:20295855-20296665 -gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc -agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca -acgcctgcatgcttccctccttccttccttccttccttcctt-ccttccttccttccttc -cttcctgcctgcctgcctgccttcctgccttcccttcctccctccctccctacctccctc -cctccttccttcccttcctccctccctcccttctttacttccttcctccttccctcctcc -tttcctccatccttccctcccttctttcctttcttcctcctgccct------ccctcctt -ctttcccttcctccctcccttccttcccatcctccttccctccct--ccttccttcctgc -cttccttccttccctccatccttccttccttccttt-cttcctccctcccttccttcctc -ccttccttcccttccttccttccctcttttccttccatctttcctttcttcctccctccc -tccctccttccctccttcattcctttct---tccctcctttccttccttcacctccttcc -cttctctcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttc -ttcacccctcccccttccctcatcccttccctccttcccttccttccttccttccctcct -tccttcccttccttccttc--cttccctccttcctt---------cccttccttccttgc -ttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgctt -ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc -tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc -ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc -ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt -taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca -gatagtcaaataactgtaa ->p:HG002_1_chr20:20295855-20296665 -gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc -agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca -acgcctgcatgcttccctccttccttccttccttccttcctt-ccttccttccttccttc -cttcctgcctgcctgcctgccttcctgccttcccttcctccctccctccctacctccctc -cctccttccttcccttcctccctccctcccttctttacttccttcctccttccctcctcc -tttcctccatccttccctcccttctttcctttcttcctcctgccct------ccctcctt -ctttcccttcctccctcccttccttcccatcctccttccctccct--ccttccttcctgc -cttccttccttccctccatccttccttccttccttt-cttcctccctcccttccttcctc -ccttccttcccttccttccttccctcttttccttccatctttcctttcttcctccctccc -tccctccttccctccttcattcctttct---tccctcctttccttccttcacctccttcc -cttctctcctcccttcatcccttccttcctttcttccttccctccctcttccttcctttc -ttcacccctcccccttccctcatcccttccctccttcccttccttccttccttccctcct -tccttcccttccttccttc--cttccctccttcctt---------cccttccttccttgc -ttccttccttccttcccttccttccttgcttccttccttccttcccttccttccttgctt -ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc -tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc -ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc -ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt -taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaaactgca -gatagtcaaataactgtaa ->p:HG002_2_chr20:20295855-20296665 -gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc -agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca -acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt -cttcctccctcccttcct---tcccttccttcccttccttccctcctttt--cttccttc -tttccttccttccttccctccctccttcccttccttccttccttcc-cttccttccttct -ctccttccttccttccctccctccttcccttccttccttctctccttccttcccttcctt -ccttctctccttccttcccttccttccttctctccttccttcccttccttccttctctcc -ttccttcccttccttccttctctccttccttcccttgcttcctttcttccttcctttgct -tccttgcttccttctttcctttcttcatccctccctccctccttccttcctttccttcct -tccctctatccttccttccttcctttctttctccctcccttccttcccttccttccttcc -ctcttttccttccatctttcctttcttcctccctccctccctccttccctccttcattac -ttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttcct -tcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatccc -ttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgctt -ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc -tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc -ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc -ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt -taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca -gatagtcaaataactgtaa ->ref_chr20:20295855-20296665 -gatgcctgtggcaggagctgagggcaagggatgagcagaggagaccaggcccctgcagcc -agaggctcagtcctggctttttccaaactcttctccagaggagcccgcccttgcacacca -acgcctgcatgcttccctccttccttccttccttccctcctttccttccttctttctttt -cttcctccctcccttcct---tcccttccttcccttccttccctcctttt--cttccttc -tttccttccttccttccctccctccttcccttccttccttc------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------cttcctccctccctccctccttccctccttcattcc -ttccttccctcctttccttccttcacctccttcccttctctcctcccttcatcccttcct -tcctttcttccttccctccctcttccttcctttcttcacccctcccccttccctcatccc -ttccctccttcccttccttccttccttccctccttccttcccttccttccttccttgctt -ccttccttctttcctttcttcatccctccttccctccctccctccttcctgccttccttc -tttctttcttttctttcttcctccctccctccttccttccctccttcctgccttccttcc -ttcctttctttttcctccctccctccttccttctttactcccttccttccttccttcctc -ccctcactcaatttgttcatcaaaaaatctagttccttgccatgccacagcctgagtatt -taaaaataacttttcctcattttagaagtaatgatcattttttaaaaattagaagctgca -gatagtcaaataactgtaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4067d52969db19e80487179e36d9331b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4067d52969db19e80487179e36d9331b.msa deleted file mode 100644 index 23d4c512..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4067d52969db19e80487179e36d9331b.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:55944162-55945285 -gtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttcttaaa -tatatatattttatatatatatagatacacacacacacacacacacacacac-------- ---------------------------atatatatatatatatatatatatatatatatat -gcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggt -gggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactccat -ctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaatcccagctact -tgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgag -atcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatatatct -atatctatagatatctatagatatatatctagatatagatctatgagtatatatctatag -atatctagatatatatttatagatagatatatctatagatatctatatatttctatcgat -agagatatctatagatatctatcaatatatctatagatttctagagatatgtatctagat -ataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaacact -ttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctatcta -gatatcggtctagatagtatctatctagatatctgtgtagatgtctagatatctatctag -atat-----tatctatctagatatctgtcgctatctagatatctatctagatatctgtcg -ctatctagatatctatctagatatctgtcgctatctagatatctatctagatagtatctg -tcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatag -tatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatct -agatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatat -ctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatct -agatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcg -ct ->syndip_2_chr20:55944162-55945285 -gtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttcttaaa -tatatatattttatatatatatagatacacacacacacacacacacacacacacacacac -acacacacacacatatatatatatatatatatatatatatatatatatatatatatatat -gcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggt -gggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactccat -ctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaatcccagctact -tgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgag -atcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatatatct -atatctatagatatctatagatatatatctagatatagatctatgagtatatatctatag -atatctagatatatatttatagatagatatatctatagatatctatatatttctatcgat -agagatatctatagatatctatcaatatatctatagatttctagagatatgtatctagat -ataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaacact -ttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctatcta -gatatcggtctagatagtatctatctagatatcggtctagat-----agtatctatctag -atatctgtgtagatgtctagatatctatctagatat---tatctatctagatatctgtcg -ctatctagatatctatctagatatctgtcgctatctagatatctatctaga---tatctg -tcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatag -tatctgtcgctatctagatatctatctagatagtatctgtcgct---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --- ->p:HG002_1_chr20:55944162-55945285 -gtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttcttaaa -tatatatattttatatatatatagatacacacacacacacacacacacacacacacacac -acacacacacacatatatatatatatatatatatatatatatatatatatatatatatat -gcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggt -gggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactccat -ctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaatcccagctact -tgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgag -atcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatatatct -atatctatagatatctatagatatatatctagatatagatctatgagtatatatctatag -atatctagatatatatttatagatagatatatctatagatatctatatatttctatcgat -agagatatctatagatatctatcaatatatctatagatttctagagatatgtatctagat -ataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaacact -ttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctatcta -gatatcggtctagatagtatctatctagatatctgtgtagatgtctagatatctatctag -atat-----tatctatctagatatctgtcgctatctagatatctatctagatatctgtcg -ctatctagatatctatctagatatctgtcgctatctagatatctatctaga---tatctg -tcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatag -tatctgtcgctatctagatatctatctagatagtatctgtcgct---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --- ->p:HG002_2_chr20:55944162-55945285 -gtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttcttaaa -tatatatattttatatatatatagatacacacacacacacacacacacacac-------- ---------------------------atatatatatatatatatatatatatatatatat -gcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggt -gggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactccat -ctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaatcccagctact -tgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgag -atcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatatatct -atatctatagatatctatagatatatatctagatatagatctatgagtatatatctatag -atatctagatatatatttatagatagatatatctatagatatctatatatttctatcgat -agagatatctatagatatctatcaatatatctatagatttctagagatatgtatctagat -ataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaacact -ttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctatcta -gatatcggtctagatagtatctatctagatatctgtgtagatgtctagatatctatctag -atat-----tatctatctagatatctgtcgctatctagatatctatctagatatctgtcg -ctatctagatatctatctagatatctgtcgctatctagatatctatctagatagtatctg -tcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatag -tatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatct -agatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatat -ctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatct -agatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcg -ct ->ref_chr20:55944162-55945285 -gtgagctgagatggcaccactgcattccagctgggcaacagagagagactctttcttaaa -tatatatattttatatatatatagatacacacacacacacacacacacacac-------- ---------------------------atatatatatatatatatatatatatatatatat -gcatgcatgccagatgcagtggctcacgcctgtaatcccagcactttgagaggccaaggt -gggcagatcatctgaggtcaggagttccagaccagcctagccaacatggtgaaactccat -ctctactaaaaatacaaaattagctggctgtggtggctcatgctggtaatcccagctact -tgggaggctgaggcaggagaatcacttgaacctgggaggtggaggttgcagtgagccgag -atcacaccactgcactccagcctggatgacagagcgagactccattaaaaaaatatatct -atatctatagatatctatagatatatatctagatatagatctatgagtatatatctatag -atatctagatatatatttatagatagatatatctatagatatctatatatttctatcgat -agagatatctatagatatctatcaatatatctatagatttctagagatatgtatctagat -ataaatctatagacatagatatagatatatagatatttaactgccaatgtcctaaacact -ttatactcaacacattttttataaaaaaaaatagatatcggtctagatagtatctatcta -gatatcggtctagatagtatctatctagatatctgtgtagatgtctagatatctatctag -atat-----tatctatctagatatctgtcgctatctagatatctatctagatatctgtcg -ctatctagatatctatctagatatctgtcgctatctagatatctatctagatagtatctg -tcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatag -tatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatct -agatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatat -ctatctagatagtatctgtcgct------------------------------------- ------------------------------------------------------------- --- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_416a8fd90bdd0755ffa5f185b247e5de.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_416a8fd90bdd0755ffa5f185b247e5de.msa deleted file mode 100644 index 8d2b70ee..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_416a8fd90bdd0755ffa5f185b247e5de.msa +++ /dev/null @@ -1,240 +0,0 @@ ->syndip_1_chr20:20356420-20357920 -ggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgagggga -ggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcaca--ctgaggggaggtggtcatagtgtgaggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtgg -tcacactggggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggt -cacactgagaggaggtggtcacactgaggggaagtggtcacactgagaggaggtggtcac -actg-------------------------------------------------------- ------------------------------------------------------------- ----------------------aggggaggtggtcatactg-------------------- ----------------------------------------tgaggggaggtggtcatactg -tgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcaca -ctgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacac -tgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacac -t----gaggggaggtggtcacactgaggggaggtggtcacagtgtgagaggaggtggtca -cactgaggggaggtggtcacagtgtga--ggggagatggtcacactgaggggaggtggtc -acagtgtgaggggaggtggtcacactgaggggaggtggtcac------------------ --agtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcac -a---------------------gtgtgaggggaggtggtcacactgaggggaggtggtca -cagtgtgaggggagatggtcacactgaggggaggtggtcacagtgtga--ggggaggtgg -tcacactgagg---------------------ggaggtggtcacagtgtgcggggaggtg -gtcatactgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtc -atactgtgagtgaggaggtagtcacactgaggggaagtggtcaca--------------- ---------ctgaggggaggtggtcacactgaggggagggggtcatactgcgagtggaggt -agtcacactgtga--agggtggtagtcacactgagaggaggtggtcacactgaggggaag -tggtcacactgaggggaggtggtcatactgtga--ggggaagtggtcacactgaggggag -gtggtcatagtgtgaggggaggtggtcaca--ctgaggggaggtggtcacactgagggga -ggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcgggg -aggtggtcatactgaggggaggtggtcacagtgtgaggggaggtggtcaca--------- -------------ctgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggg -aggtggtcacactgagggg----------------------------------------- -------------------aggtggtcacactgtgaggggaggtggtcacactgaggagag -gtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca--ctgaggaga -ggtggtcatagtgtgaggggaggtggtcacac--tgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgagggg -aggtggtcacagtg--------------------------------------tgagggga -ggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggag -gtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgagggga -ggtggtcacattgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggag -gtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagagg -tggtcatagtgtgcggggaggtggtcacactgaggggaggtggtcacactgaggggaggt -ggtcacagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggagg -tggtcatagtgtgaggggaggtggtcacactgagggg ->syndip_2_chr20:20356420-20357920 -ggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcacagtg-------- ------------tgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtgg -tcacactggggaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggt -cacactgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcat -agtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcaca -ctgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacac -tgagaggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactg -tgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcaca -ctgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacac -tgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacac -t----gaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtca -tactgaggggaggtggtcacagtgtga--ggggaggtggtcacactgaggggaggtggtc -acagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtca -tagtgtgaggggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcac -actgaggggaggtggtcatactgtgagtgaggaagtagtcacactgaggggaagtggtca -ca--ctgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtag -tcacactgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggta -gtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtc -atactgtga--ggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtg -gtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactg--aggggaggt -ggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacactgaggggagg -tggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggag -ggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagagga -ggtggtcaca--ctgaggggaagtggtcacactgaggggaggtggtcatactgtgagggg -aagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgagggga -ggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcgggg -aggtggtcatactgagggg----------------------------------------- -------------------aggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcacagtgtgcggggaggtggtcacactgaggggaggtggtcatagtgtgagggga -ggtggtcata--ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggag -aggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgagggg -aggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacactgagggga -ggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtgacactgaggggag -gtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgagggga -ggtggtcacattgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggag -gtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagagg -tggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggt -ggtcacagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggagg -tggtcatagtgtgaggggaggtggtcacactgagggg ->p:HG002_1_chr20:20356420-20357920 -ggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcacagtg-------- ------------tgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtgg -tcacactggggaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggt -cacactgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcat -agtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcaca -ctgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacac -tgagaggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactg -tgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcaca -ctgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacac -tgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacac -t----gaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcacagtgtga--ggggaggtggtcacactgaggggaggtggtc -acagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtca -tagtgtgaggggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcac -actgaggggaggtggtcatactgtgagtgaggaagtagtcacactgaggggaagtggtca -ca--ctgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtag -tcacactgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggta -gtcacactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtc -atactgtga--ggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtg -gtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactg--aggggaggt -ggtcatactgtgtgcggggaggtggtcatactgaggggaggtggtcacactgaggggagg -tggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggag -ggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagagga -ggtggtcaca--ctgaggggaagtggtcacactgaggggaggtggtcatactgtgagggg -aagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgagggga -ggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcgggg -aggtggtcatactgagggg----------------------------------------- -------------------aggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcacagtgtgcggggaggtggtcacactgaggggaggtggtcatagtgtgagggga -ggtggtcata--ctgaggggaggtggtcacactgtgaggggaggtggtcacactgaggag -aggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgagggg -aggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacactgagggga -ggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtgacactgaggggag -gtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgagggga -ggtggtcacattgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggag -gtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagagg -tggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggt -ggtcacagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggagg -tggtcatagtgtgaggggaggtggtcacactgagggg ->p:HG002_2_chr20:20356420-20357920 -ggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgagggga -ggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtgg -tcacactggggaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggt -cacactgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcat -agtg-------------------------------------------------------- ------------------------------------------------------------- ----------------------aggggaggtggtcacagtg-------------------- ----------------------------------------tgaggggaggtggtcatactg -tgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcaca -ctgtgaagggtggtagtcacactgaggggaggtggtcacactggggaggtggtcacactg -tgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca-- -ctgaggggaagtggtcacactgagaggaggtggtcaca--ctgaggggaggtggtcatac -tgtgagtgaggaggtagtcacactgaggggaagtggtcaca--ctgaggggaggtggtca -cactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtc -atactgcgagtggaggtagtcacactgtgaagggtggtagtc------------------ --acactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcat -a---------------------ctgtgaggggaagtggtcacactgaggggaggtggtca -tagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtga--ggggaggtgg -tcacactgagg---------------------ggaggtggtcacagtgtgcggggaggtg -gtcatactgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtc -atactgtgagtgaggaggta---------------------------------------- ----------------------gtcacactgaggggagggggtcatactgcgagtggaggt -agtcacactgtga--agggtggtagtcacactgagaggaggtggtcacactgaggggaag -tggtcacactgaggggaggtggtcatactgtga--ggggaagtggtcacactgaggggag -gtggtcatagtg---------------------tgaggggaggtggtcacactgagggga -ggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgaggggag -gtggtcacagtgtgaggggaggtggtcaca--ctgaggggaggtggtcaca--------- -----------gtgtacggggaggtggtcatactgaggggaggtggtcacagtgtgagggg -aggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgtgagggga -ggtggtcacactgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagag -gtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca--ctgaggaga -ggtggtcatagtgtgaggggaggtggtcacac--tgaggggaggtggtcacactgagggg -aggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggg -gaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgagggg -aggtggtcacagtg--------------------------------------tgagggga -ggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggag -gtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgagggga -ggtggtcacattgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggag -gtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagagg -tggtcatagtgtgcggggaggtggtcacactgcggggaggtggtcatactgaggggaggt -ggtcacagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggagg -tggtcatagtgtgaggggaggtggtcacactgagggg ->ref_chr20:20356420-20357920 -ggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggag -gtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgagggga -ggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact----ggggaggt -ggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtg -gtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtgg -tcacactggggaggtggtcacactgtgaggggaggtggtcacac--tgagaggaggtggt -cacactgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcat -agtg-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------tgaggggaggtggtcacactggggaggtggtcacactg -tgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca-- -ctgaggggaagtggtcacactgagaggaggtggtcaca--ctgaggggaggtggtcatac -tgtgagtgaggaggtagtcacactgaggggaagtggtcaca--ctgaggggaggtggtca -cactgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtc -atactgcgagtggaggtagtcacactgtgaagggtggtagtc------------------ --acactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcat -a---------------------ctgtgaggggaagtggtcacactgaggggaggtggtca -tagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtga--ggggaggtgg -tcacactgagg---------------------ggaggtggtcacagtgtgcggggaggtg -gtcatactgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtc -atactgtgagtgaggaggta---------------------------------------- ----------------------gtcacactgaggggagggggtcatactgcgagtggaggt -agtcacactgtga--agggtggtagtcacactgagaggaggtggtcacactgaggggaag -tggtcacactgaggggaggtggtcatactgtga--ggggaagtggtcacactgaggggag -gtggtcatagtg---------------------tgaggggaggtggtcacactgagggga -ggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcgggg -aggtggtcatactgaggggaggtggtcacagtgtgaggggaggtggtcaca--------- -----------gtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgagggg -aggtggtcacactgagggg----------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4248c4ccdcf22249a1ca92c0fca9a551.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4248c4ccdcf22249a1ca92c0fca9a551.msa deleted file mode 100644 index 999ea0d2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4248c4ccdcf22249a1ca92c0fca9a551.msa +++ /dev/null @@ -1,260 +0,0 @@ ->syndip_1_chr20:63491489-63493164 -gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc -actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc -tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg -gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg -gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg -gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg -aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg -gatggatggggggatagatggatggatggatggatggatggacggacg----gatgggga -ggtggatggatggatggatggatggatggatggatggatgaggagatgaatggatggatg -agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga -ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg -gggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggga -gatggatggatggatggatggggagggatggatggatggatggatggatgggtggatgga -tagaaggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatgga -tagatggata----gatggatggatggatggatggatggagagaaggatggatgggtggg -gaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgga -tggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggg -gaggtgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatgga -tggatggatgcatggatggatgga------------------------------------ ------------------------------------------------------------- --------------------tggagaggtgggtggacggatggatggattgggaggtgggt -agatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggat -ggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggac -agaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggat -ggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggac -gggtggggagatggatggatggatggatggatggatggatggatggacagaaggatgtat -gggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaa -ggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggat -gggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggt -gggacaatagatggatggatagagagaaggatggatgggtggggagatggatggatggat -ggatggatggatggatggatggatggatagagagaaggatggatggttgagaca----at -ggatggatggatggatggagagatggatggatggacggatggacagaaggatggatgggt -ggggaggtggatggatggattgaaggatggatgggtgggga----catggatggatggat -ggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggata--- ------gatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggt -ggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggat -gaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggatagag -agaaggatggatgggtggggagatggatggatggatggatggatggatggatagagagaa -ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat -ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat -ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat -ggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggat -ggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatggat -ggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggag -agatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatggat -ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat -agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg -ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg -tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc -tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcgg ->syndip_2_chr20:63491489-63493164 -gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc -actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc -tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg -gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg -gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg -gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg -aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg -gatggatggggggatagatggatggatggatggatggacggacggatggggaggtggatg -gatggatggatggatggatggatggatggatggatggatgaggagatgaatggatggatg -agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga -ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg -gggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggga -gatggatggatggatggatgcggagggatggatggatggatggatggatgggtggatgga -tagaaggatggatgggtggggaggtgggtgggtgggtgcgtggatggatggagagatgga -tagatggatagatggatggatggatggatggatggatggagagaaggatggatgggtggg -gaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgga -tggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggg -gaggtgggtgggtggatggatggatgagtggggaggtgggtgggtggatggatggatgga -tggatgcatggatggatggatggagaggtgggtggatgggtggatggacagaaggatgga -tgggtggggaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatgga -tggatgaaggatggatgggtggggaggtgggtggacggatggatggattgggaggtgggt -agatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggat -ggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggac -agaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggat -ggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggac -gggtgggga----gatggatggatggatggatggatggatggatggacagaaggatgtat -gggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaa -ggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggat -gggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggt -gggacaatagatggatggatagagagaaggatggatgggtgggga--------gatggat -ggatggatggatggatggatggatggatagagagaaggatggatggttgagacaatggat -ggatggatggatggatggagagatggatggatggatggatggacagaaggatggatgggt -ggggaggtggatggatggattgaaggatggacgggtggggagatggatggatggatggat -ggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggatagat -ggatggatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggt -ggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggat -gaatggatggatggatagatagaaggatggatgggtgggacaaca----gatggatagag -agaaggatggatgggtgggga----gatggatggatggatggatggatggatagagagaa -ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat -ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat -ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat -ggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggat -ggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatggat -ggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggag -agatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatggat -ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat -agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg -ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg -tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc -tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcgg ->p:HG002_1_chr20:63491489-63493164 -gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc -actggctgggggtctcctatcagtgcccttctctggggtctcagatttgtttatggtttc -tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg -gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg -gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg -gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg -aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg -gatggatggggggatagatggatggatggatggatggacggacggatggggaggtggatg -gatggatggatggatggatggatggatggatggatggatgaggagatgaatggatggatg -agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga -ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg -gggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggga -gatggatggatggatggatgcggagggatggatggatggatggatggatgggtggatgga -tagaaggatggatgggtggggaggtgggtgggtgggtgcgtggatggatggagagatgga -tagatggatagatggatggatggatggatggatggatggagagaaggatggatgggtggg -gaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgga -tggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggg -gaggtgggtgggtggatggatggatgagtggggaggtgggtgggtggatggatggatgga -tggatgcatggatggatggatggagaggtgggtggatgggtggatggacagaaggatgga -tgggtggggaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatgga -tggatgaaggatggatgggtggggaggtgggtggacggatggatggattgggaggtgggt -agatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggat -ggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggac -agaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggat -ggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggac -gggtgggga----gatggatggatggatggatggatggatggatggacagaaggatgtat -gggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaa -ggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggat -gggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggt -gggacaatagatggatggatagagagaaggatggatgggtgggga--------gatggat -ggatggatggatggatggatggatggatagagagaaggatggatggttgagacaatggat -ggatggatggatggatggagagatggatggatggatggatggacagaaggatggatgggt -ggggaggtggatggatggattgaaggatggacgggtggggagatggatggatggatggat -ggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggatagat -ggatggatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggt -ggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggat -gaatggatggatggatagatagaaggatggatgggtgggacaaca----gatggatagag -agaaggatggatgggtgggga----gatggatggatggatggatggatggatagagagaa -ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat -ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat -ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat -ggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggat -ggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatggat -ggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggag -agatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatggat -ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat -agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg -ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg -tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc -tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcgg ->p:HG002_2_chr20:63491489-63493164 -gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc -actggctgggggtctcctatcagtgcccttctctggggtctcagatttgtttatggtttc -tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg -gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg -gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg -gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg -aatggatggatggggaggtggatggatagatggatggatggatggatggatggatggatg -gatggatggggggatagatggatggatggatggatggatggacggacg----gatgggga -ggtggatggatggatggatggatggatggatggatggatgaggagatgaatggatggatg -agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga -ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg -gggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggga -gatggatggatggatggatggggagggatggatggatggatggatggatgggtggatgga -tagaaggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatgga -tagatggata----gatggatggatggatggatggatggagagaaggatggatgggtggg -gaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgga -tggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtggg -gaggtgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatgga -tggatggatgcatggatggatgga------------------------------------ ------------------------------------------------------------- --------------------tggagaggtgggtggacggatggatggattgggaggtgggt -agatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggat -ggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggac -agaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggat -ggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggac -gggtggggagatggatggatggatggatggatggatggatggatggacagaaggatgtat -gggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaa -ggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggat -gggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggt -gggacaatagatggatggatagagagaaggatggatgggtggggagatggatggatggat -ggatggatggatggatggatggatggatagagagaaggatggatggttgagaca----at -ggatggatggatggatggagagatggatggatggacggatggacagaaggatggatgggt -ggggaggtggatggatggattgaaggatggatgggtgggga----catggatggatggat -ggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggata--- ------gatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggt -ggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggat -gaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggatagag -agaaggatggatgggtggggagatggatggatggatggatggatggatggatagagagaa -ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat -ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat -ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat -ggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggat -ggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatggat -ggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggag -agatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatggat -ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat -agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg -ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg -tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc -tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcgg ->ref_chr20:63491489-63493164 -gtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagccc -actggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggtttc -tcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggatg -gatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggtg -gggagatggatgagtagggagatggatggatggattggtggatggatggatggatggatg -gatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggatg -aatggatggatggggaggtggatggata----gatggatggatggatggatggatggatg -gatggatggggggatagatggatggatggatggatggacggacggatggggaggtggatg -gatggatggatggatggatggatggatggatggatggatgaggagatgaacggatggatg -agatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagaga -ggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatg -gggaggtggatggat--------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------ggatgtat -gggtgggtaggtgggtggatagatggatg------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------gatggatggatggataaatggatggatggaaggatggatggataggtaggtgggt -ggatggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggat -gaatggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagag -agaaggatggatgggtgggta----gatggatggatggatggatggatggatagagagaa -ggatggatggttgagacaatggatggatggatggatggatggagagatggatggatggat -ggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatggat -ggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatggat -ggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatggat -ggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatggat -ggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatggag -agatggagggatggttcgatagagagaa----ggatggatgggacaatggatggatggat -ggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatggat -agatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggatg -ggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgtg -tggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggtc -tagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaat -cttgtacacgtcctgcagcgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_428eb0dfcca6a3ca33b28ed002f2c4b1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_428eb0dfcca6a3ca33b28ed002f2c4b1.msa deleted file mode 100644 index 51ea4523..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_428eb0dfcca6a3ca33b28ed002f2c4b1.msa +++ /dev/null @@ -1,130 +0,0 @@ ->syndip_1_chr20:60314333-60314821 -aaaatccatccatctgtcctcctacccatcctgctatccatccatccatccatcctccca -taatctatcttcccatccatttgtccttccttccttccttccttccttccttcttccttc -cttccttccttccttccttccacccatccatcctcccattcatcctcccatgcatcctcc -catccatccacccaaccatcctcccatccatcctcacatcgatcttcgcatccatccatc -gatcgatctatccatccatccatccatcctcccatccatcctcccatccattatcccatt -catccatcctcccatccatcctcctatccatccatccatccatccaccctcccatccatc -catcctcccatccatccactcttccatccatccatccacccaccctt------------- ----ccatccatccatcctcccatccatccatcctcccattcatctatccatccatccctc -gatcctcccatccatccatcctcccatccatccatccatcctcccatccatccatccacc -ctcccatccatccatcctcccatccatctaccctcccatccatccatcctcccacccacc -ctcccatccatccatcctcccatcctcccatccatccatccatcctcccatccgtccatc -catccttccatccac----------------cctcccatccatccatcctcccatccatc -taccctcccatccatccatcctcccacccaccctcccatccatccaccctcccatccatc -catcctcccatccatctatccatccatcctcccatcctcccatccatccatcatccatcc -atccatccatccatcctcccataatctatcttcccatccatttgtccttccttccttcct -tccttccttccttccttcgttccacccatccatcctcccattcatcctcccatgcatcct -cccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccatcca -tccatccatccatctatccat--------------------ccatcctcccatccatcct -cccatcctcccatccattctcccattcatccatcctcccatccatcctcctatccatcca -tccatccatccaccctcccatccatccatcctcccatccatccacccttccatccatcca -tccacccacccttccatccatccaccctcccatccatccatcctcccattcatctatcca -tccatccctcgatcctcccatccatccatccatcctcccatccgtccatccatccttcca -tccaccctcccatccatccatcctcccatccatctaccctcccatccatccatcctccca -cccaccctcccatccatccaccctcccatccatccatcctcccatccatctatccatcca -tcctcccatcctcccatcctcccatccatccatccatccatccatccatcctcccatcc ->syndip_2_chr20:60314333-60314821 -aaaatccatccatctgtcctcctacccatcctgctatccatccatccatccatcctccca -taatctatcttcccatccatttgtccttc-----------------------cttccttc -cttccttccttccttccttccacccatccatcctcccatgcatcctcccatgcatcctcc -catccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccatccatc -catccatctatccatccatccatccatcctcccatccatcctcccatccattatcccatt -catccatcctcccatccatcctcctatccatccatccatccatccaccctctcatccatc -catcctcccatccatccacccttccatccatccatccacccacccttccatccatccatc -ctcccatccatccatcctcccatccatccatcctcccattcatctatccatccatccctc -gatcctcccatccatccatcctcccatccatccatccatcctcccatccatccatccacc -ctcccatccatccatcctcccatccatctaccctcccatccatccatcctcccatccacc -ctcccatccatccatccatccatccaccctctcatccatccatcctcccatccgtccatc -catccttccatccaccctcccatccatccatcctcccatccatccatcctcccatccatc -taccctcccatccatccatcctcccacccaccctcccatccatccaccctcccatccatc -catcctcccatccatctatccatccatcctcccatcctcccatccatccatcatccatcc -atccatccatccatcctcccataatctatcttcccatccatttgtccttccttccttcct -tccttccttcc--------ttccacccatccatcctcccattcatcctcccatgcatcct -cccatccatccacccaaccatcctcccatccatcctcacatcgatcttcgcatccatcca -tcgatcgatctatccatccatccatcctcccatccatcctcccatcctcccatccatcct -cccatcctcccatccattctcccattcatccatcctcccatccatcctcctatccatcca -tccatccatccaccctcccatccatccatcctcccatccatccacccttccatccatcca -tccacccacccttccatccatccaccctcccatccatccatcctcccattcatctatcca -tccatccctcgatcctcccatccatccatccatcctcccatccgtccatccatccttcca -tccaccctcccatccatccatcctcccatccatctaccctcccatccatccatcctccca -cccaccctcccatccatccaccctcccatccatccatcctcccatccatctatccatcca -tcctcccatcctcccatcctcccatccatccatccatccatccatccatcctcccatcc ->p:HG002_1_chr20:60314333-60314821 -aaaatccatccatctgtcctcctacccatcctgctatccatccatccatccatcctccca -taatctatcttcccatccatttgtccttccttccttccttccttccttccttcttccttc -cttccttccttccttccttccacccatccatcctcccattcatcctcccatgcatcctcc -catccatccacccaaccatcctcccatccatcctcacatcgatcttcgcatccatccatc -gatcgatctatccatccatccattc----------------------------tcccatt -catccatcctcccatccatcctcctatccatccatccatccatccaccctcccatccatc -catcctcccatccatccacccttccatccatccatccacccacccttccatccatccatc -ctcccatccatccatcctcccatccatccatcctcccattcatctatccatccatccctc -gatcctcccatccatccatcctcccatccatccatccatcctcccatccatccatccacc -ctcccatccatccatcctcccatccatctaccctcccatccatccatcctcccatccacc -ctcccatccatccatccatccatccaccctctcatccatccatcctcccatccgtccatc -catccttccatccaccctcccatccatccatcctcccatccatccatcctcccatccatc -taccctcccatccatccatcctcccacccaccctcccatccatccaccctcccatccatc -catcctcccatccatctatccatccatcctcccatcctcccatccatccatcatccatcc -atccatccatccatcctcccataatctatcttcccatccatttgtccttccttccttcct -tccttccttcc--------ttccacccatccatcctcccattcatcctcccatgcatcct -cccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccatcca -tccatccatccatctatccatccatcctcccatccatcctcccatcctcccatccatcct -cccatcctcccatccattctcccattcatccatcctcccatccatcctcctatccatcca -tccatccatccaccctcccatccatccatcctcccatccatccacccttccatccatcca -tccacccacccttccatccatccaccctcccatccatccatcctcccattcatctatcca -tccatccctcgatcctcccatccatccatccatcctcccatccgtccatccatccttcca -tccaccctcccatccatccatcctcccatccatctaccctcccatccatccatcctccca -cccaccctcccatccatccaccctcccatccatccatcctcccatccatctatccatcca -tcctcccatcctcccatcctcccatccatccatccatccatccatccatcctcccatcc ->p:HG002_2_chr20:60314333-60314821 -aaaatccatccatctgtcctcctacccatcctgctatccatccatccatccatcctccca -taatctatcttcccatccatttgtccttccttccttccttccttccttccttcttccttc -cttccttccttccttccttccacccatccatcctcccattcatcctcccatgcatcctcc -catccatccacccaaccatcctcccatccatcctcacatcgatcttcgcatccatccatc -gatcgatctatccatccatccattctcccattcatccatcctcccatccatcctcctatc -catccatccatccatccaccctcccatccatccatcctcccatccaccctcccatccatc -catcctcccatccatccactcttccatccatccatccacccaccctt------------- ----ccatccatccatcctcccatccatccatcctcccattcatctatccatccatccctc -gatcctcccatccatccatcctcccatccatccatccatcctcccatccatccatccacc -ctcccatccatccatcctcccatccatctaccctcccatccatccatcctcccacccacc -ctcccatccatccatcctcccatcctcccatccatccatccatcctcccatccgtccatc -catccttccatccac----------------cctcccatccatccatcctcccatccatc -taccctcccatccatccatcctcccacccaccctcccatccatccaccctcccatccatc -catcctcccatccatctatccatccatcctcccatcctcccatccatccatcatccatcc -atccatccatccatcctcccataatctatcttcccatccatttgtccttccttccttcct -tccttccttccttccttcgttccacccatccatcctcccattcatcctcccatgcatcct -cccatccatccacccaaccatcctcccatccatcctcacatccatcttcgcatccatcca -tccatccatccatctatccat--------------------ccatcctcccatccatcct -cccatcctcccatccattctcccattcatccatcctcccatccatcctcctatccatcca -tccatccatccaccctcccatccatccatcctcccatccatccacccttccatccatcca -tccacccacccttccatccatccaccctcccatccatccatcctcccattcatctatcca -tccatccctcgatcctcccatccatccatccatcctcccatccgtccatccatccttcca -tccaccctcccatccatccatcctcccatccatctatccacccttccatccatccatcca -cccacccttccatccatccaccctcccatccatccatcctcccatccatctatccatcca -tcctcccatcctcccatcctcccatccatccatccatccatccatccatcctcccatcc ->ref_chr20:60314333-60314821 -aaaatccatccatctgtcctcctacccatcctgctatccatccatccatccatcctccca -taatctatcttcccatccatttgtccttccttccttccttccttccttccttcttccttc -cttccttccttccttccttccacccatccatcctcccattcatcctcccatgcatcctcc -catccatccacccaaccatcctcccatccatcctcacatcgatcttcgcatccatccatc -gatcgatctatccatccatccattc----------------------------tcccatt -catccatcctcccatccatcctcctatccatccatccatccatccaccctcccatccatc -catcctcccatccatccacccttccatccatccatccacccacccttccatccatccacc -ctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcctcc -catccatccatccatccatccatccatcctcccatcc----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_452bf94642317f3790592594df0a74e2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_452bf94642317f3790592594df0a74e2.msa deleted file mode 100644 index d9ae6133..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_452bf94642317f3790592594df0a74e2.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:63221380-63221976 -tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga -tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc -gcagtagcttc------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------ggactgcagggactgcagggat -tgcagggactgcagggattgcagggactgcagggattgcagggattgcagggattgcagg -gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc -ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt -gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg -gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc ->syndip_2_chr20:63221380-63221976 -tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga -tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc -gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggag -tgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagg -gactgcagggactgcagggactgcagggattgcagggactgcagggactgcagggattgc -agggattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggac -tgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcagg -gattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactgc -agggattgcagggattgcagggattgcagggattgcagggattgcagggactgcagggac -tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg -gactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattgc -agggattgcagggactgcagggactgcagggactgcagggattgcagggattgcagggat -tgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgcagg -gattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggacacc -ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt -gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg -gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc ->p:HG002_1_chr20:63221380-63221976 -tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga -tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc -gcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcagggag -tgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgcagg -gactgcagggactgcagggactgcagggattgcagggactgcagggactgcagggattgc -agggattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggac -tgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcagg -gattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactgc -agggattgcagggattgcagggattgcagggattgcagggattgcagggactgcagggac -tgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagg -gactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattgc -agggattgcagggactgcagggactgcagggactgcagggattgcagggattgcagggat -tgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgcagg -gattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggccacc -ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt -gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg -gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc ->p:HG002_2_chr20:63221380-63221976 -tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga -tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc -gcagtagcttc------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------ggactgcagggactgcagggat -tgcagggactgcagggattgcagggactgcagggattgcagggattgcagggattgcagg -gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggccacc -ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt -gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg -gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc ->ref_chr20:63221380-63221976 -tcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccga -tgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcatc -gcagtagcttc------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------ggactgcagggattgcagggactgcagggattgcagggattgcagg -gattgcagggactgcagggattgcagggactgcagggactgcagggactgcagggactgc -agggactgcagggattgcagggattgcagggattgcagggactgcagggattgcagggac -tgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattgcagg -gattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacacc -ttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctggt -gaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcggg -gccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4c116e15ba8ab8e716088527ed87a481.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4c116e15ba8ab8e716088527ed87a481.msa deleted file mode 100644 index 9b934518..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4c116e15ba8ab8e716088527ed87a481.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:62349531-62349936 -actatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtca -tggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaacccaggggatgg -ggatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatgg -tgatggtgatggtgatggtgatggtgggggtggtgat---------ggtgggggtggggg -tggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgg -gggtgatgatggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgat -gatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtgggggtgg--gggt -gatgacggtgat---------------------ggtgggggtgatgacggtgggggtggg -ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt -gggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgag -ggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgggagtgggggtg -atgacggtgatggtgggggtgatgacggtgatggtgggggtgatgacggtgatggcggtg -ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggg -gtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtg -ggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatg -gtgggggtgatggtgggggtgggggtggg---------ggtgggggtgatgatggtgatg -gtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtgggggtg--- ------------ggggtgggggtgatgacggtgatggtgggggtgatgatggtgggagtgg -gctggtagtgggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcag -aaaattgctgg------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------ctgatg -acatgga ->syndip_2_chr20:62349531-62349936 -actatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtca -tggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaaccca------gg -ggatggggatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatgg -tgggggtgatgatggtgatggtgatggtgatggtgat---------------ggtggggg -tggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgg -gggtgatgatggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgat -gatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtgggggtgg--gggt -gatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg -ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt -gggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgag -ggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtg -atgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtg -ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggg -gtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtg -ggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatg -gtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtgatgatggtgatg -gtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggg -gtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatgacggtgggagtgg -g--ggtgatgacggtgatggtgggggtgatgac--ggtgatggtgggggtgatgacggtg -atggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggtgggggtg -ggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatg -gtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagtgggggtga -tggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctggctgatg -acatgga ->p:HG002_1_chr20:62349531-62349936 -actatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtca -tggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaaccca------gg -ggatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatgg -tgatggtgatggtgatggtgatggtgggggtggtgat--------------gggtggggg -tgatgacggtgggagtgggggtgatgacggtgatggtgggggtgatgacggtgatggtgg -gggtgatgatggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgat -gatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtgggggtgg--gggt -gatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg -ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt -gggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgag -ggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtg -atgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtg -ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggg -gtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtg -ggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatg -gtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtgatgatggtgatg -gtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggggtgggggtgggg -gtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatgacggtgggggtgg -g--ggtgatgacggtgatggtgggggtgatgac--gatgatggtgggggtgatgacggtg -atggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggtgggggtg -ggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatg -gtgggggtggcggtgatggtgggggtgatgatggtgggagtgggctggtagtgggggtga -tggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctggctgatg -acatgga ->p:HG002_2_chr20:62349531-62349936 -actatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtca -tggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaaccca------gg -ggatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatgg -tgatggtgatggtgatggtgatggtgggggtggtgatggtggtgatggtgggggtggggg -tggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatgacggtggggctgg -gggtgatgatggtgggggtgatgacggtgatgatgggggtggaggggtgatgacggtgat -gatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtgggggtgg--gggt -gatgacggtgat---------------------ggtgggggtgatgacggtgggggtggg -ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt -gggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtgatgatggtgag -ggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgggggtgggggtg -atgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacggtgatggcggtg -ggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggg -gtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtg -ggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtagaggtgatgatg -gtgggggtgatggtgggggtgggggtggg---------ggtgggggtgatgatggtggtg -ggggtgatgacggtgggagtgggggtgatgacggtgatggtgggggtgatgacggtg--- ------------atggtgggggtgatgacggtgatggtgggggtgatgatggtgggagtgg -gctggtagtgggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcag -aaaattgctgg------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------ctgatg -acatgga ->ref_chr20:62349531-62349936 -actatcattcaagagggaggacaaaacagccgttttcagacaattccggatagactgtca -tggaatagaaaaactacagggtgcatttcaggaaggaggaagcagcaaccca------gg -ggatggggatggggatggggatggtgggggtgatgggggtgatgatggtgatggtgatgg -tgatggtgatggtgatggtgatggtgggggtggtgat--------------gggtggggg -tgatgacggtgggagtgggggtgatgacggtgatggtgggggtgatgacggtgatggtgg -gggtgatgacggtgatggtgggggtgatgatggtgggagtgggctggtagtgggggtgat -ggtttgggtgggagtaaggtgatg-----gtggaggtaaagaggcagaaaattgctggct -gatgacatgga------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4c62e9e567847f11b5b3b70d5d98b983.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4c62e9e567847f11b5b3b70d5d98b983.msa deleted file mode 100644 index f047a50e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4c62e9e567847f11b5b3b70d5d98b983.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:278819-279179 -ctcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagg -aagcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggag -ggcgggacggagggagggagggcggga------------gggagggacggagggaggaag -ggcgggacggacggagggagggagggagggacggagggcgggacggcgggagggcgggac -ggagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggag -ggagggcgggacggag----------------ggagggagggagggagggacggagggcg -ggacggagggagggaggg-----cggagggagggagggcgggacggagggagggagggcg -ggacggagggtg------------ggagggagggagggatggagggagggagggagggac -ggagggcgggacggagggacggagggagggagggagggacggaggttgggacggagggac -ggagggcggg-------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------cgga -tgccgcgggtctcaccgccaggg ->syndip_2_chr20:278819-279179 -ctcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagg -aagcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggag -ggcgggacggagggagggagggcgggacggagggagggagggagggcgggacggagggag -ggagggcgggacggagggagggagggagggacggagggcgggacggcgggagggcgggac -ggagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggag -ggagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcg -ggacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcg -ggacggagggagggagggcgggacggagggacggagggagggagggcgggacggagggag -ggagggcgggacggagggacggagggagggagggcgggacggagggagggagggagggac -ggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagggcg -ggagggagggagggcgggacggagggagggagggagggagggcgggacggagggagggag -ggagggagggacggagggacggagggagggagggagggagggacggagggcgggacggag -ggagggagggcggagggagggagggcgggacggagggagggagggagggacggagggcgg -gacggagggagggagggcggagggagggagggcgggacggagggagggagggcgggaggg -atggagggagggagggcgggacggagggagggcgggagggagggacggagggcgggacgg -agggacggagggagggagggagggacggaggttgggacggagggacggagggcgggcgga -tgccgcgggtctcaccgccaggg ->p:HG002_1_chr20:278819-279179 -ctcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagg -aagcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggag -ggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcgggag -ggagggcgggacggagggagggagggagggacggagggcgggacggcgggagggcgggac -ggagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggag -ggagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcg -ggacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcg -ggacggagggagggagggcgggacggagggacggagggagggagggcgggacggagggag -ggagggcgggacggagggacggagggagggagggcgggacggagggagggagggagggac -ggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggagggcg -ggagggagggagggcgggacggagggagggagggagggagggcgggacggagggagggag -ggagggagggacggagggacggagggagggagggagggagggacggagggcgggacggag -ggagggagggcggagggagggagggcgggacggagggagggagggagggacggagggcgg -gacggagggagggagggcggacggcgggagggcgggacggagggacggagggagggcggg -acggagggcgggagggcgggacggagggagggagggagggagggacggagggcgggacgg -agggacggagggagggagggagggacggaggttgggacggagggacggagggcgggcgga -tgccgcgggtctcaccgccaggg ->p:HG002_2_chr20:278819-279179 -ctcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagg -aagcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggag -ggcgggacggagggagggagggcggga------------gggagggacggagggaggaag -ggcgggacggacggagggagggagggagggacggagggcgggacggcgggagggcgggac -ggagggacggagggagggcgggacggagggcgggagggcgggacggagggagggagggag -ggagggcgggacggag----------------ggagggagggagggagggacggagggcg -ggacggagggagggaggg-----cggagggagggagggcgggacggagggagggagggcg -ggacggagggtg------------ggagggagggagggatggagggagggagggagggac -ggagggcgggacggagggacggagggagggagggagggacggaggttgggacggagggac -ggagggcggg-------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------cgga -tgccgcgggtctcaccgccaggg ->ref_chr20:278819-279179 -ctcttgcaaagcccaggtgaggggagtgaagggtgaagaaatgcgtcttccaggtggagg -aagcaccacgtgcagtgggcggggaaaggcaggagagggcgcgcgagtgcgcggagggag -ggcgggacggagggagggagggcg------------------------------------ ---------ggacggagggagggagggagggacggagggcgggacggcgggagggcgggac -ggagggacggagggagggcgggacggagggcgggagggcgggacggag------------ ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------ggagggagggagggagggac -ggagggcgggacggagggacggagggagggagggagggacggaggttgggacggagggac -ggagggcggg-------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------cgga -tgccgcgggtctcaccgccaggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4eee85d5b4dd5f6e65e1aa2a72f439df.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4eee85d5b4dd5f6e65e1aa2a72f439df.msa deleted file mode 100644 index 25be5099..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4eee85d5b4dd5f6e65e1aa2a72f439df.msa +++ /dev/null @@ -1,205 +0,0 @@ ->syndip_1_chr20:63948414-63948858 -acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca -agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc -catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga --ggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggagggg -cgtgtgtgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtgaggggcgtg -tgtgagagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgtg -agaggtaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagag -gg-----------------aggggcgtgtgtgtgagggaggggcgtgtgagag-ggaggg -ggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgt -gtgagagggagggggcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt--- --gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaga -cggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagg -gaggggcgtgtgtgagggagggg---gcgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggaggggg -cgtgtgtgagagggaggggcgtgtgagaggg-aggggcgtgtgtgagagg---------- -gagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaaggga -ggggcgtgtgtgagagggagggggcgtgagagggaggggcgtgtgtgagagggaggggcg -tgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg -tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtga -gag--------ggagggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgtg -tgtgagaggga-ggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtg -agagggagggggcgtgtgtgagagggagggggcgtgt-------------gtgagaggga -gaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggagagg -cgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcg -tgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtg -agagggaggggcgtgtgtgagagggag--------------ggggcgtgtgtgagaggga -ggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga-g -gggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcg -tgtgtgagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgaga -gggagggggcgtg-----agagggaggggcgtgtgtgagagggaggggcgtgtgtgagag -ggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagaggg -aggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggg --gcgtgtgagagggaggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcgt -gtgtgagaggga-ggggcgtgtgtgagagggagggg-cgtgtgtgagagggaggggcgtg -agagggagggggcgtgtgt--gagggaggggcgtgtgtgagaggga-ggggggcgtgtgt -gagagggagggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa -gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc -tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctg ->syndip_2_chr20:63948414-63948858 -acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca -agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc -catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga -gggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggagggg -cgtgtgtgagagggagggggcgtgtgtgaaagggaggggcgtgtgtgagggaggggcgtg -tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgtg -agagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgaggg -ggggcgtgtgtgagagggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggagg -ggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgt -gtgag-gggggggcgtgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtgag -agggagggggcgtgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga-- --agggaggggtgtgtgtgagagtgggggcgtgtgtgagaggg--------gcgtgagagg -taggggcgtgtgtgagagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga- -ggggcgtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgtgagggaggggg -cgtgtgtgagagggaggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtga -gggggggcgtgtgtgagaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-aggga -ggggcgtgtgtgagaggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggcg -tgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg -tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgagg -ggggcgtgtgagagggaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgtg -tgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtg -tgaagggaggggtgtgtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggta -ggggcgtgtgtgagagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggagggg -cgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcg -tgtgtgagggagggggcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgag-ggagggggcgtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgtg -agaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtga---ggg -ggggcgtgtgtgagaggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggagg -gggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt--------------- -----------------gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaga -gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-ag -ggaggggcgtgtgtgagagtgggggcgtgtgtgagaggg----------gcgtgagaggt -aggggcgtgtgtgagagggagggg-gcgtgagagggaggggcgtgtgtgagagggagggg -cgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgt -gtgtgagagggagggggcgtgtgtgagagggagggg-cgtgt---------------gtg -agagggaaggggcgtgtga--gagggaggggcgtgtgtgagaggga-ggggcgtgtgtga -ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa -gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc -tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctg ->p:HG002_1_chr20:63948414-63948858 -acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca -agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc -catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga -gggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggagggg -cgtgtgtgagagggagggggcgtgtgtgaaagggaggggcgtgtgtgagggaggggcgtg -tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgtg -agagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgaggg -ggggcgtgtgtgagagggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggagg -ggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgt -gtgag-gggggggcgtgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtgag -agggagggggcgtgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga-- --agggaggggtgtgtgtgagagtgggggcgtgtgtgagaggg--------gcgtgagagg -taggggcgtgtgtgagagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga- -ggggcgtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgtgagggaggggg -cgtgtgtgagagggaggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtga -gggggggcgtgtgtgagaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-aggga -ggggcgtgtgtgagaggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggcg -tgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg -tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgagg -ggggcgtgtgagagggaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgtg -tgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtg -tgaagggaggggtgtgtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggta -ggggcgtgtgtgagagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggagggg -cgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcg -tgtgtgagggagggggcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgag-ggagggggcgtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgtg -agaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtga---ggg -ggggcgtgtgtgagaggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggagg -gggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt--------------- -----------------gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaga -gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-ag -ggaggggcgtgtgtgagagtgggggcgtgtgtgagaggg----------gcgtgagaggt -aggggcgtgtgtgagagggagggg-gcgtgagagggaggggcgtgtgtgagagggagggg -cgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgt -gtgtgagagggagggggcgtgtgtgagagggagggg-cgtgt---------------gtg -agagggaaggggcgtgtga--gagggaggggcgtgtgtgagaggga-ggggcgtgtgtga -ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa -gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc -tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctg ->p:HG002_2_chr20:63948414-63948858 -acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca -agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc -catgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggga --ggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggagggg -cgtgtgtgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtgaggggcgtg -tgtgagagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgtg -agaggtaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagag -gg-----------------aggggcgtgtgtgtgagggaggggcgtgtgagag-ggaggg -ggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgt -gtgagagggagggggcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt--- --gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaga -cggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagg -gaggggcgtgtgtgagggagggg---gcgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggaggggg -cgtgtgtgagagggaggggcgtgtgagaggg-aggggcgtgtgtgagagg---------- -gagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaaggga -ggggcgtgtgtgagagggagggggcgtgagagggaggggcgtgtgtgagagggaggggcg -tgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtg -tgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtga -gag--------ggagggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgtg -tgtgagaggga-ggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtg -agagggagggggcgtgtgtgagagggagggggcgtgt-------------gtgagaggga -gaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggagagg -cgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcg -tgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgt -gtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtg -agagggaggggcgtgtgtgagagggag--------------ggggcgtgtgtgagaggga -ggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga-g -gggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcg -tgtgtgagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgaga -gggagggggcgtg-----agagggaggggcgtgtgtgagagggaggggcgtgtgtgagag -ggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagaggg -aggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggg --gcgtgtgagagggaggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcgt -gtgtgagaggga-ggggcgtgtgtgagagggagggg-cgtgtgtgagagggaggggcgtg -agagggagggggcgtgtgt--gagggaggggcgtgtgtgagaggga-ggggggcgtgtgt -gagagggagggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa -gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc -tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctg ->ref_chr20:63948414-63948858 -acagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagca -agctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgc -catgcgcctcg------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---gtgtgaggagggaggcgtgtgtgagagggaggggatgtgt---------------gtg -agagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaaggggcgtgtgtga -ga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaa -gggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcactc -tctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcaggt -gccactttgttgccataaaccaaaccgtagtctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_4f621d80726125d4b530e4a698e371ee.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_4f621d80726125d4b530e4a698e371ee.msa deleted file mode 100644 index 95751805..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_4f621d80726125d4b530e4a698e371ee.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:62830511-62830939 -ccccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccga -ggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctct -acccatgtaccacagtcccccaccccccaccgtgctccacc------------------- ------------------------ccccaccacagtcccccaccccccaccccagtcccca -aacccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccc -accccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgcca -acccccatgacagtccctca--------------------acccccaccacagtccccca -acccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccac -cccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca- -cccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaa -atctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactg -tggcgcctttggcccctctgaccttcca ->syndip_2_chr20:62830511-62830939 -ccccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccga -ggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctct -acccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccc -aaacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccc -aacccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcc -aacccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgcca -acccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtccccca -acccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccac -cccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccac -cccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaa -atctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactg -tggcgcctttggcccctctgaccttcca ->p:HG002_1_chr20:62830511-62830939 -ccccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccga -ggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctct -acccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccc -aaacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccc -aacccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcc -aacccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgcca -acccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtccccca -acccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccac -cccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccac -cccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaa -atctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactg -tggcgcctttggcccctctgaccttcca ->p:HG002_2_chr20:62830511-62830939 -ccccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccga -ggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctct -acccatgtaccacagtcccccaccccccaccgtgctccacc------------------- ------------------------ccccaccacagtcccccaccccccaccccagtcccca -aacccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccc -accccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgcca -acccccatgacagtccctca--------------------acccccaccacagtccccca -acccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccac -cccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca- -cccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaa -atctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactg -tggcgcctttggcccctctgaccttcca ->ref_chr20:62830511-62830939 -ccccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccga -ggtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctct -acccatgtaccacagtccccc--------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------acccccatgacagtccccca -acccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccac -cccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccac -cccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaa -atctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactg -tggcgcctttggcccctctgaccttcca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_50a9c4a3245e4f0c0cab0597a64af000.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_50a9c4a3245e4f0c0cab0597a64af000.msa deleted file mode 100644 index b4fced49..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_50a9c4a3245e4f0c0cab0597a64af000.msa +++ /dev/null @@ -1,105 +0,0 @@ ->syndip_1_chr20:62875072-62875656 -aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac -cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt -catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac -ccccacccccacccgcacccccacccccacccgcacccccacccccacccccacccgcac -ccccacccccacccccacccgcacccccacccccacccgcacccccacccccacccccac -ccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgcac -ccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccgcac -ccgcacccccacccccaccctcacccgcacccgcacccccacccccacccccacccgcac -ccgcacccccacccccacccc------------cacccccacccccacccgcacccgcac -ccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgcacccccac -ccgcacccccacccccacccccacccccacccgcacccgcacccccacccccacccccac -ccccacccccacccccacccccacccccaccctcacccgcacccccaccctcacccccac -cctcacccccaccctcacccgcaccctcacccgcacccgcacccccaccct------cac -ccacaccctcacccccaccctcacccccacccccaccctcacccgcacccgcacccccac -cctcacccccacccccacccccaccctcaccctcaccctcacccgcacccgcacccccac -ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac -ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc -acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact -gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgc ->syndip_2_chr20:62875072-62875656 -aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac -cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt -catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac -ccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgcac -ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgcac -ccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcacccccac -ccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgcac -ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccccac -ccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcacccccac -ccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgcac -ccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgcac -ccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcacccccac -cctcacccccaccctcacccgcacccccacccccacccccacccccaccctcccccccac -ccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccac -cctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctcac -ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac -ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc -acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact -gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgc ->p:HG002_1_chr20:62875072-62875656 -aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac -cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt -catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac -ccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgcac -ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgcac -ccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcacccccac -ccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgcac -ccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccccac -ccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcacccccac -ccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgcac -ccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgcac -ccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcacccccac -cctcacccccaccctcacccgcacccccacccccacccccacccccaccctcccccccac -ccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccac -cctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctcac -ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac -ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc -acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact -gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgc ->p:HG002_2_chr20:62875072-62875656 -aactttcctggcacactggagaggacggcagaacgctggaatggatttatcgtgcaagac -cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt -catcggggagccccgcaccctcacctgcaccctcacccccacccccacccccacccccac -ccccacccccacccgcacccccacccccacccgcacccccacccccacccccacccgcac -ccccacccccacccccacccgcacccccacccccacccgcacccccacccccacccccac -ccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgcac -ccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccgcac -ccgcacccccacccccaccctcacccgcacccgcacccccacccccacccccacccgcac -ccgcacccccacccccacccc------------cacccccacccccacccgcacccgcac -ccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgcacccccac -ccgcacccccacccccacccccacccccacccgcacccgcacccccacccccacccccac -ccccacccccacccccacccccacccccaccctcacccgcacccccaccctcacccccac -cctcacccccaccctcacccgcaccctcacccgcacccgcacccccaccct------cac -ccacaccctcacccccaccctcacccccacccccaccctcacccgcacccgcacccccac -cctcacccccacccccacccccaccctcaccctcaccctcacccgcacccgcacccccac -ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac -ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc -acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact -gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgc ->ref_chr20:62875072-62875656 -aactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaagac -cagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaatt -catcggggagc------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------cccgcaccctcacctgcaccctcac -ccccacccccacccccacccccacccccacccgcacccccacccccaccctcccccccac -ccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcacccccac -cctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctcac -ccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctcac -ccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacaccc -acatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaact -gctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcgggag -ctatcctgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5179b77bf332da7c07500c14adccd838.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5179b77bf332da7c07500c14adccd838.msa deleted file mode 100644 index f9079649..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5179b77bf332da7c07500c14adccd838.msa +++ /dev/null @@ -1,180 +0,0 @@ ->syndip_1_chr20:38123490-38124805 -ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg -gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg -tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa -taatatataataataatatataatatgtataataataatatataatatttataataataa -tatatataatatgtatatataatatacatatacctattatatataatatacctattatat -ataatatacatatacctattatatataatatacctattatatataagatacctattatat -ataatatacatatacctattatatatataatatacctattatatatatataatataccta -ttatatataatatacctattatatatataatatacctattatatatataatatacctatt -atatatataatatacctattatatataatatacctattatatataaaatatacctattat -atataatatacctattatatacattatatataatatacctattatatgcattatatataa -tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc -tattatatgcattatatataatatacctattatatgcattatataatatattatatataa -tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta -ttatatattatatattatatatataatatacatattatatgtattatatattatatataa -tatacatattatatattatatattatatacatattatatattatatattatatacatatt -atatattatatacatattatatattatatattatatacatattatacattatatatatct -aaaatatataatacacattatatattatataatacacattatatataatatataatacac -attatatattatatataatacacattatatattatatataatacacattatatat----- -------------------tatataatacacattatatattatatataatacacattatat -attatatataatacacattatatattatatataatacacattatatattatataatacac -attatatattatatataatacacattatatatataatacacattatatattatatataat -acataatacacattatatattatatataatacacattatatataatatataacacacatt -atatataatatataacacacattatatattatatataatacacattatatattatatata -atacacatatattatatataatacacattatatattatatataatacacatatattatat -ataatacacattatatattatatataatacacattatatataatatataatacacattat -atataatacttattatatattatacataatatacatattatatataatacataatatacg -tatattatataatatacatattatatataatacataatatacgtatattatataatatac -atattatatatattatactatatataatactcatatatatacatattatatatacatatt -atatataatactcatattatatgtacatattatacatacatattatatataatacacata -tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat -tatatatgtattatattattatagatataatatacatattatatctatatataaaatata -tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca -atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc -cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtca ->syndip_2_chr20:38123490-38124805 -ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg -gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg -tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa -taatatataataataatatataatatgtataataataatatataatatttataataataa -tatatataatatgtatatataatatacatatacctattatatataatatacctattatat -ataatatacatatacctattatatataatatacctattatatataagatacctattatat -ataatatacatatacctattatatatataatatacctattatatatatataatataccta -ttatatataatatacctattatatatataatatacctattatatatataatatacctatt -atatatataatatacctattatatataatatacctattatatataaaatatacctattat -atataatatacctattatata---------------------------cattatatataa -tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc -tattatatgcattatatataatatacctattatatgcattatataatatattatatataa -tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta -ttatatattatatattatatatataatatacatattatatgtattatatattatatataa -tatacatattatatattatatattatatacatattatatattatatattatatacatatt -atatattatatacatattatatattatatattatatacatattatacattatatatatct -aaaatatataatacacattatatattatataatacacattatatataatatataatacac -attatatattatatataatacacattatatattatatataatacacattatatattatat -aatacacattatatattatatataatacacattatatattatatataatacacattatat -attatatataatacacattatatattatatataatacacattatatattatataatacac -attatatattatatataatacacattatatatataatacacattatatattatatataat -acataatacacattatatattatatataatacacattatatataatatataacacacatt -atatataatatataacacacattatatattatatataatacacattatatattatatata -atacacatatattatatataatacacattatatattatatataatacacatatattatat -ataatacacattatatattatatataatacacattatatataatatataatacacattat -atataatacttattatatattatacataatatacatattatatataatacataatatacg -tatattatataatatacatattatatataatacataatatacgtatattatataatatac -atattatatatattatactatatataatactcatatatatacatattatatatacatatt -atatataatactcatattatatgtacatattatacatacatattatatataatacacata -tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat -tatatatgtattatattattatagatataatatacatattatatctatatataaaatata -tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca -atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc -cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtca ->p:HG002_1_chr20:38123490-38124805 -ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg -gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg -tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa -taatatataataataatatataatatgtataataataatatataatatttataataataa -tatatataatatgtatatataatatacatatacctattatatataatatacctattatat -ataatatacatatacctattatatataatatacctattatatataagatacctattatat -ataatatacatatacctattatatatataatatacctattatatatatataatataccta -ttatatataatatacctattatatatataatatacctattatatatataatatacctatt -atatatataatatacctattatatataatatacctattatatataaaatatacctattat -atataatatacctattatata---------------------------cattatatataa -tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc -tattatatgcattatatataatatacctattatatgcattatataatatattatatataa -tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta -ttatatattatatattatatatataatatacatattatatgtattatatattatatataa -tatacatattatatattatatattatatacatattatatattatatattatatacatatt -atatattatatacatattatatattatatattatatacatattatacattatatatatct -aaaatatataatacacattatatattatataatacacattatatataatatataatacac -attatatattatatataatacacattatatattatatataatacacattatatattatat -aatacacattatatattatatataatacacattatatattatatataatacacattatat -attatatataatacacattatatattatatataatacacattatatattatataatacac -attatatattatatataatacacattatatatataatacacattatatattatatataat -acataatacacattatatattatatataatacacattatatataatatataacacacatt -atatataatatataacacacattatatattatatataatacacattatatattatatata -atacacatatattatatataatacacattatatattatatataatacacatatattatat -ataatacacattatatattatatataatacacattatatataatatataatacacattat -atataatacttattatatattatacataatatacatattatatataatacataatatacg -tatattatataatatacatattatatataatacataatatacgtatattatataatatac -atattatatatattatactatatataatactcatatatatacatattatatatacatatt -atatataatactcatattatatgtacatattatacatacatattatatataatacacata -tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat -tatatatgtattatattattatagatataatatacatattatatctatatataaaatata -tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca -atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc -cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtca ->p:HG002_2_chr20:38123490-38124805 -ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg -gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg -tcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatataa -taatatataataataatatataatatgtataataataatatataatatttataataataa -tatatataatatgtatatataatatacatatacctattatatataatatacctattatat -ataatatacatatacctattatatataatatacctattatatataagatacctattatat -ataatatacatatacctattatatatataatatacctattatatatatataatataccta -ttatatataatatacctattatatatataatatacctattatatatataatatacctatt -atatatataatatacctattatatataatatacctattatatataaaatatacctattat -atataatatacctattatatacattatatataatatacctattatatgcattatatataa -tatacctattatatgcattatatataatatacctattatatgcattatatataatatacc -tattatatgcattatatataatatacctattatatgcattatataatatattatatataa -tatgcatattatatgtattatatattatatattatatatataatatacatattatatgta -ttatatattatatattatatatataatatacatattatatgtattatatattatatataa -tatacatattatatattatatattatatacatattatatattatatattatatacatatt -atatattatatacatattatatattatatattatatacatattatacattatatatatct -aaaatatataatacacattatatattatataatacacattatatataatatataatacac -attatatattatatataatacacattatatattatatataatacacattatatat----- -------------------tatataatacacattatatattatatataatacacattatat -attatatataatacacattatatattatatataatacacattatatattatataatacac -attatatattatatataatacacattatatatataatacacattatatattatatataat -acataatacacattatatattatatataatacacattatatataatatataacacacatt -atatataatatataacacacattatatattatatataatacacattatatattatatata -atacacatatattatatataatacacattatatattatatataatacacatatattatat -ataatacacattatatattatatataatacacattatatataatatataatacacattat -atataatacttattatatattatacataatatacatattatatataatacataatatacg -tatattatataatatacatattatatataatacataatatacgtatattatataatatac -atattatatatattatactatatataatactcatatatatacatattatatatacatatt -atatataatactcatattatatgtacatattatacatacatattatatataatacacata -tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat -tatatatgtattatattattatagatataatatacatattatatctatatataaaatata -tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca -atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc -cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtca ->ref_chr20:38123490-38124805 -ttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgtg -gatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcctg -tcctgtaacctctctgggcctcagaaacctctctctctctctatatatatatatatataa -taatatataataataatatataatatgtataataataatatataatatttataataataa -tatatataatatgtatatataatatacatatacctattatatataatatacctattatat -ataatatacataaacctattatatataatatacctattatatataagatacctattatat -ataatatacctat------------------------------tatatataagataccta -ttatatataatatac--------------atatacctattatatatataatatacctatt -ata----------------tatatataatatacctattatatatataatatacctatta- ----------------------------------------------------tatatataa -tatacctattatatatataata-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------tacctattatatataatacacattatatataatatataacacacatt -atatataatatataacacacattatatattatatataatacacattatatattatatata -atacacatatattatatataatacacattatatattatatataatacacatatattatat -ataatacacattatatattatatataatacacattatatataatatataatacacattat -atataatacttattatatattatacataatatacatattatatataatacataatatacg -tatattatataatatacatattatatataatacataatatacgtatattatataatatac -atattatatatattatactatatataatactcatatatatacatattatatatacatatt -atatataatactcatattatatgtacatattatacatacatattatatataatacacata -tatacatattatatataatacacacacacattatatatgtcttatatataatatacatat -tatatatgtattatattattatagatataatatacatattatatctatatataaaatata -tatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgca -atcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagccccc -cgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttattttttg -tagagatggggtttcgccatgttgccgaggctggtgtca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5436e349b375c3c3c5c78f37e14a447d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5436e349b375c3c3c5c78f37e14a447d.msa deleted file mode 100644 index 575face8..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5436e349b375c3c3c5c78f37e14a447d.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:23155403-23156076 -ggggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttc -tgtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgc -cctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaagg -ggaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggg -agggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaagga -aagaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaagga -aggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaag -agagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagg -aaggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaa -gagaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaa -gagaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaa -ggaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaa -gaaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaa -ggtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttag -ggagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcc -tgcaaagccccca ->syndip_2_chr20:23155403-23156076 -ggggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttc -tgtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgc -cctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaagg -ggaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggg -agggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaagga -aagaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaagga -aggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaag -agagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagg -aaggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaa -g----agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaa -gagaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaa -ggaaagaaag------------------------aagaaagaaagaaagaaagaaagaaa -gaaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaa -ggtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttag -ggagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcc -tgcaaagccccca ->p:HG002_1_chr20:23155403-23156076 -ggggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttc -tgtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgc -cctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaagg -ggaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggg -agggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaagga -aagaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaagga -aggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaag -agagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagg -aaggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaa -g----agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaa -gagaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaa -ggaaagaaag------------------------aagaaagaaagaaagaaagaaagaaa -gaaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaa -ggtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttag -ggagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcc -tgcaaagccccca ->p:HG002_2_chr20:23155403-23156076 -ggggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttc -tgtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgc -cctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaagg -ggaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggg -agggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaagga -aagaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaagga -aggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaag -agagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagg -aaggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaa -gagaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaa -gagaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaa -ggaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaa -gaaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaa -ggtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttag -ggagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcc -tgcaaagccccca ->ref_chr20:23155403-23156076 -ggggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttc -tgtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgc -cctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaagg -ggaggggaggaaggga-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------aggaaaagagagagaaagagaaag -agagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagg -aaggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaa -g--------agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaa -gagaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaa -ggaaagaaag------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaa -gaaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaa -ggtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttag -ggagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcc -tgcaaagccccca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_560824ad2ee0cf0cbf7c99308e508c6a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_560824ad2ee0cf0cbf7c99308e508c6a.msa deleted file mode 100644 index 4d1a0c1b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_560824ad2ee0cf0cbf7c99308e508c6a.msa +++ /dev/null @@ -1,200 +0,0 @@ ->syndip_1_chr20:22082156-22084015 -atgtataatatatgtatatataatatatgtatatactatacatgtatatattatattata -catgtatatattataagtatatactatacatgcatgtattatatgtatatactatacatg -catgtattatatgtatatattatacatgcatgtattatatgtatatattatacatgcatg -tattatatgtatatattatacatgtatgtattatatgtatagattatacatgtatatatt -atatatgtatatattacacatgtacatatatgtatatattaaacacgtttatattattta -ttatacatgactatattatataggtatatatgatatatgcatatatgtcatataggtata -tatgacatatatgcatatatcatgtaggtatatatgacatatgcatatatcatataggta -tatatgacatatgcatatatcatataggtatatatgatatatgcgcatatatcatatagg -tatatatgatatatgcgcatatatcatataggtatatatgatatatgcgcatat------ ----atcatataggtatatatgatatatgcgcatatatcatataggtatatatgatatatg -cgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatatatgata -tatgcgcatatatcatacaggtatatgcgcatatatcatataggtataggtataggtaga -tatatgatatatgcacacatatcatataggtatatatgatatatg------------ata -ggtatatatgatatatgataggtatatatgatatatgataggtatatatgatatatatca -tatcggtatatatgatatatatcatatcggtatatataggtatatatcataggtatatat -aggtatatatcacataggtatatataggtatatatcatataggtatatataatatatgca -tttatattatataggtatatatattacataggtatatgtaatatgtgcatatatattata -taggtatatatattatacaggcatatataatacgtatatatattatatgggcatatatat -gtgtatatattatataggtatatataatatatgtgtatatattatgtgggtatatataat -atatgtgtacatattatgtgggtatatataatatatgtgtacatattatgtgggtatata -taatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatgtgggta -tatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatattatgtg -ggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatatta -tgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatat -attatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgt -atatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatat -gtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaataggaag -caggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatat -tatatatacg---------------------------------tatattaatatagacgt -atatataatatatacatatatacatatatagtatatactatgtatacatatatactatac -atacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgtatacata -tatactatatatacatacattatatacatacattatatatgtgtattatatatgtatata -ttatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtctcatta -taccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttcctattacat -atatattatatagatacatatataatatatacatatatactacataatatatgcatatat -aatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatat -aatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatat -aatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatat -aatatatacatatg ->syndip_2_chr20:22082156-22084015 -atgtataatatatgtatatataatatatgtatatactatacatgtatatattatattata -catgtatatattataagtatatactatacatgcatgtattatatgtatatac-------- ---------------------tatacatgcatgtattatatgtatatattatacatgcatg -tattatatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtatt -atatgtatagat------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------tatacatgtatatattatatatg -tatatattacacatgtacatatat-------gtatatattaaacacgtttatattattta -ttatacatgtaggtatatatgacatat--gcatatatcatataggtatatatgacatat- --gcatatatcatataggtatatatgatatatgcgcatatatcatataggtatatatgata -tatgcgcatatatcatacaggtatatgcgcatatatcatataggtataggtataggtaga -tatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatata -ggtatatatgatatatgataggtatatatgatatatgataggtatatatgatatatatca -tatcggtatatatgatatatatcatatcggtatatataggtatatatcataggtatatat -aggtatatatcacataggtatatataggtatatatcatataggtatatataatatatgca -tttatattatataggtatatatattacataggtatatgtaatatgtgcatatatattata -taggtatatatattatacaggcatatataatacgtatatatattatatgggcatatatat -gtgtatatattatataggtatatataatatatgtgtatatattatgtgggtatatataat -atatgtgtatatattatgtgggtatatataatatatgtgtacatattatgtgggtatata -taatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggta -tatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgta -ggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatatta -tgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatat -attatgtaggtatatataatatatgtgtatatattatatatgta---------------- ------------------------------------------------------------- -----------------------------------------------------ataggaag -caggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatat -tatatatacgtatattaatatagacgtatatataatatatacatatattaatatagacgt -atatataatatatacatatatacatatatagtatatactatgtatacatatatactatac -atacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgtatacata -tatactatatatacatacattatatacatacattatatatgtgtattatatatgtatata -ttatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtctcatta -taccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttcctattacat -atatattatatagatacatatataatatatacatatatactacataatatatgcatatat -aatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatat -aatatatacatatgttgtatatgtatatataatatatacatatg---------------- ------------------------------------------------------------- --------------- ->p:HG002_1_chr20:22082156-22084015 -atgtataatatatgtatatataatatatgtatatactatacatgtatatattatattata -catgtatatattataagtatatactatacatgcatgtattatatgtatatac-------- ---------------------tatacatgcatgtattatatgtatatattatacatgcatg -tattatatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtatt -atatgtatagat------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------tatacatgtatatattatatatg -tatatattacacatgtacatatat-------gtatatattaaacacgtttatattattta -ttatacatgtaggtatatatgacatat--gcatatatcatataggtatatatgacatat- --gcatatatcatataggtatatatgatatatgcgcatatatcatataggtatatatgata -tatgcgcatatatcatacaggtatatgcgcatatatcatataggtataggtataggtaga -tatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatata -ggtatatatgatatatgataggtatatatgatatatgataggtatatatgatatatatca -tatcggtatatatgatatatatcatatcggtatatataggtatatatcataggtatatat -aggtatatatcacataggtatatataggtatatatcatataggtatatataatatatgca -tttatattatataggtatatatattacataggtatatgtaatatgtgcatatatattata -taggtatatatattatacaggcatatataatacgtatatatattatatgggcatatatat -gtgtatatattatataggtatatataatatatgtgtatatattatgtgggtatatataat -atatgtgtatatattatgtgggtatatataatatatgtgtacatattatgtgggtatata -taatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggta -tatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgta -ggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatatta -tgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatat -attatgtaggtatatataatatatgtgtatatattatatatgta---------------- ------------------------------------------------------------- -----------------------------------------------------ataggaag -caggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatat -tatatatacgtatattaatatagacgtatatataatatatacatatattaatatagacgt -atatataatatatacatatatacatatatagtatatactatgtatacatatatactatac -atacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgtatacata -tatactatatatacatacattatatacatacattatatatgtgtattatatatgtatata -ttatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtctcatta -taccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttcctattacat -atatattatatagatacatatataatatatacatatatactacataatatatgcatatat -aatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatat -aatatatacatatgttgtatatgtatatataatatatacatatg---------------- ------------------------------------------------------------- --------------- ->p:HG002_2_chr20:22082156-22084015 -atgtataatatatgtatatataatatatgtatatactatacatgtatatattatattata -catgtatatattataagtatatactatacatgcatgtattatatgtatatactatacatg -catgtattatatgtatatattatacatgcatgtattatatgtatatattatacatgcatg -tattatatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtatt -atatgtatagatattacacatgtacatatatgtatatattaaacacgtttatattattta -ttatacatgactatattatataggtatatatgatatatgcatatatgtcatataggtata -tatgacatatatgcatatatcatgtaggtatatatgacatatgcatatatcatataggta -tatatgacatatgcatatatcatataggtatatatgatatacatgtatatattatatatg -tatatattacacatgtacatatat-------gtatatattaaacacgtttatattattta -ttatacatgtaggtatatatgacatat--gcatatatcatataggtatatatgacatat- --gcatatatcatataggtatatatgatatatgcgcatatatcatataggtatatatgata -tatgcgcatatatcatacaggtatatgcgcatatatcatataggtataggtataggtaga -tatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatata -ggtatatatgatatatgataggtatatatgat-----ataggtatatatgatatatatca -tatcggtatatatgatatatatcatatcggtatatataggtatatatcataggtatatat -aggtatatatcacataggtatatataggtatatatcatataggtatatataatatatgca -tttatattatataggtatatatattacataggtatatgtaatatgtgcatatatattata -taggtatatatattatacaggcatatataatacgtatatatattatatgggcatatatat -gtgtatatattatataggtatatataatatatgtgtatatattatgtgggtatatataat -atatgtgtatatattatgtgggtatatataatatatgtgtacatattatgtgggtatata -taatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggta -tatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgta -ggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatatta -tgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatat -attatgtaggtatatataatatatgtgtatatattatatatgtatatataatatatgtgt -atatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatat -gtgtatatattatgtaggt---------------------------------ataggaag -caggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatat -tatatatacgtatattaatatagacgtatatataatatatacatatattaatatagacgt -atatataatatatacatatatacatatatagtatatactatgtatacatatatactatac -atacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgtatacata -tatactatatatacatacattatatacatacattatatatgtgtattatatatgtatata -ttatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtctcatta -taccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttcctattacat -atatattatatagatacatatataatatatacatatatactacataatatatgcatatat -aatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatat -aatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatat -aatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatat -aatatatacatatg ->ref_chr20:22082156-22084015 -atgtataatatatgtatatataatatatgtatatactatacatgtatatattatattata -catgtatatattataagtatatactatacatgcatgtattatatgtatatactatacatg -catgtattatatgtatatattatacatgcatgtattatatgtatatattatacatgcatg -tattatatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtatt -atatgtatagat------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------tatacatgtatatattatatatg -tatatattacacatgtacatatat-------gtatatattaaacacgtttatattattta -ttatacatgtaggtatatatgacatat--gcatatatcatataggtatatatgacatat- --gcatatatcatataggtatatatgatatatgcgcatatatcatataggtatatatgata -tatgcgcatatatcatacaggtatatgcgcatatatcatataggtataggtataggtaga -tatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatata -ggtatatatgatatatgataggtatatatgatatatgataggtatatatgatatatatca -tatcggtatatatgatatatatcatatcggtatatataggtatatatcataggtatatat -aggtatatatcacataggtatatataggtatatatcatataggtatatataatatatgca -tttatattatataggtatatatattacataggtatatgtaatatgtgcatatatattata -taggtatatatattatacaggcatatataatacgtatatatattatatgggcatatatat -gtgtatatattatataggtatatataatatatgtgtatatattatgtgggtatatataat -atatgtgtatatattatgtgggtatatataatatatgtgtacatattatgtgggtatata -taatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggta -tatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatattatgta -ggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatatatta -tgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtatat -attatgtaggtatatataatatatgtgtatatattatatatgta---------------- ------------------------------------------------------------- -----------------------------------------------------ataggaag -caggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgagaaatat -tatatatacgtatattaatatagacgtatatataatatatacatatattaatatagacgt -atatataatatatacatatatacatatatagtatatactatgtatacatatatactatac -atacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgtatacata -tatactatatatacatacattatatacatacattatatatgtgtattatatatgtatata -ttatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtctcatta -taccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttcctattacat -atatattatatagatacatatataatatatacatatatactacataatatatgcatatat -aatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgtatatat -aatatatacatatgttgtatatgtatatataatatatacatatg---------------- ------------------------------------------------------------- --------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_588376aafa87a62eea70f0f3200a73be.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_588376aafa87a62eea70f0f3200a73be.msa deleted file mode 100644 index c93ff493..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_588376aafa87a62eea70f0f3200a73be.msa +++ /dev/null @@ -1,170 +0,0 @@ ->syndip_1_chr20:4032118-4033702 -ccgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgca -gcggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaa -agagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctc -tgcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctgga -aagt----------------------------------------gaggagcgtctctgcc -cggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagg -aagtgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccc -caccgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggt -gaggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaac -cgccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgag -gagcgtctccgcccggcagccaccccgtccgggagggaggtggggggggtcagccccccg -cccggccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactggg -aagtgaggagcccctctgcccggccagccgccccgtccgggagggaggcggggggggggg -tcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccg -ccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggtcagtcccccgcccggc -cggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagcccccc -gcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagc -cgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccg -ggagggaggtggg--ggggggtcagccccccgcccggccagccgccccgtccgggaggga -ggtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctc -tgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccg -ggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtc -agccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgcc -cctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggg -ggggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccg -gccgcccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggaggg -tagtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgctt -ctgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctg -ggaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaa -tagaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtg -gatggaagtagacatg ->syndip_2_chr20:4032118-4033702 -ccgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgca -gcggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaa -agagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctc -tgcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctgga -aagtgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcc -cggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagg -aactgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccc -caccgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggt -gaggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaac -cgccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgag -gagcgtctccgcccggcagccaccccgtccgggagggaggt------------------- ------------------------------------------------------------- --------------------------------------------------ggggggggggg -tcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccg -ccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggc -cggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagcccccc -gcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagc -cgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccg -ggagggaggtgggggggggggtcagccccccgcccggccagccgccccgtccgggaggga -ggtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctc -tgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccg -ggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtc -agccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgcc -cctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggg -ggggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccg -gccgcccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggaggg -tagtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgctt -ctgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctg -ggaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaa -tagaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtg -gatggaagtagacatg ->p:HG002_1_chr20:4032118-4033702 -ccgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgca -gcggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaa -agagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctc -tgcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctgga -aagtgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcc -cggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagg -aactgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccc -caccgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggt -gaggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaac -cgccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgag -gagcgtctccgcccggcagccaccccgtccgggagggaggt------------------- ------------------------------------------------------------- --------------------------------------------------ggggggggggg -tcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccg -ccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggc -cggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagcccccc -gcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagc -cgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccg -ggagggaggtgggggggggggtcagccccccgcccggccagccgccccgtccgggaggga -ggtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctc -tgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccg -ggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtc -agccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgcc -cctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggg -ggggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccg -gccgcccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggaggg -tagtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgctt -ctgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctg -ggaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaa -tagaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtg -gatggaagtagacatg ->p:HG002_2_chr20:4032118-4033702 -ccgggattgcagatgaagtctcgttcactcagtgctcaatggtgcccaggctggagtgca -gtggcgtgatctccgctcgctacaacctccacctcccagccgcctgccttggcctcccaa -agagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctc -tgcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctgga -aagt----------------------------------------gaggagcgtctctgcc -cggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagg -aagtgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccc -caccgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggt -gaggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaac -cgccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgag -gagcgtctccgcccggcagccaccccgtccgggagggaggtggggggggtcagccccccg -cccggccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactggg -aagtgaggagcccctctgcccggccagccgccccgtccgggagggaggcggggggggggg -tcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccg -ccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggtcagtcccccgcccggc -cggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagcccccc -gcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagc -cgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccg -ggagggaggtggg--ggggggtcagccccccgcccggccagccgccccgtccgggaggga -ggtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctc -tgcccggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccg -ggagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtc -agccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgcc -cctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggg -ggggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccg -gccgcccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggaggg -tagtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgctt -ctgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctg -ggaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaa -tagaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtg -gatggaagtagacatg ->ref_chr20:4032118-4033702 -ccgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgca -gcggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaa -agagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctc -tgcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctgga -aagtgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcc -cggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagg -aactgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgccc -caccgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggt -gaggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaac -cgccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgag -gagcgtctccgcccggcagccaccccgtccgggagggaggt------------------- ------------------------------------------------------------- --------------------------------------------------ggggggggggg -tcggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccg -ccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggaccc -ctctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggc -cggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtga -ggagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagcccccc -gcctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagc -cgccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccg -ggagggaggtggg----------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------gggggggtc -agccccctttccggccg--ccgcctgtccgggaggtgaggggcgcctctgcctggccgcc -cctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtggg -ggggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccg -gccgcccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggaggg -tagtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgctt -ctgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctg -ggaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaa -tagaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtg -gatggaagtagacatg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5adf27fe85d81caa84eca9adf8dc6fbc.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5adf27fe85d81caa84eca9adf8dc6fbc.msa deleted file mode 100644 index a8a7c9b7..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5adf27fe85d81caa84eca9adf8dc6fbc.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:21721341-21721756 -tgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatataatacat -atatatacatatatattatatatgtaatacatatataatatatatgtaatgtatatatat -gtaatgtatataatatatatgtaatacatatataatatatatgtaatgtatataatatat -atgtaatacatatataatatatatgtaatgtatattatatatgtaatgtatataatatgt -atgtaatacatatattatatatgtaatgt--atattatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtaatacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatataa -catatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaat -acatatataac----atgtattacatatatgtaatacatatataac-------------- -------------atgtattacatatatgtaatacatatataac----atgtattacatat -atgtaatacacatataatatatatgttatatatatatatatatataaaattttttaaaaa -attgtttcttgagatagggtctcactctgtcacccag ->syndip_2_chr20:21721341-21721756 -tgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatataatacat -atatatacatatatattatatatgtaatacatatataatatatatgtaatgtatatatat -gtaatgtatataatatatatgtaatacatatataatatatatgtaatgtatataatatat -atgtaatacatatataatatatatgtaatgtatattatatatgtaatgtatataatatgt -atgtaatacatatattatatatgtaatgt--atattatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtattacatatataacatatatgtattacatatatgtaat -acatatataacatatatgtattacatatatgtaatacatatataacatatatgtaataca -tatataacatatatgtattacatatatgtaatacatatataac----atgtattacatat -atgtaatacacatataatatatatgttatatatatatatatatataaaattttttaaaaa -attgtttcttgagatagggtctcactctgtcacccag ->p:HG002_1_chr20:21721341-21721756 -tgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatataatacat -atatatacatatatattatatatgtaatacatatataatatatatgtaatgtatatatat -gtaatgtatataatatatatgtaatacatatataatatatatgtaatgtatat--tatat -atgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatattatatat -gtattacatatatgtattacatatataac--atattatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtattacatatataacatatatgtattacatatatgtaat -acatatataacatatatgtattacatatatgtaatacatatataacatatatgtaataca -tatataac----atgtattacatatatgtattacatatataacatatatgtattacatat -atgtaatacacatataatatatatgttatatatatatatatatataaaattttttaaaaa -attgtttcttgagatagggtctcactctgtcacccag ->p:HG002_2_chr20:21721341-21721756 -tgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatataatacat -atatatacatatatattatatatgtaatacatatataatatatatgtaatgtatatatat -gtaatgtatataatatatatgtaatacatatataatatatatgtaatgtatat--tatat -atgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatattatatat -gtattacatatatgtattacatatataacatatatgtattacatattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtaatacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatataa -catatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaat -acatatataac----atgtattacatatatgtaatacatatataac-------------- -------------atgtattacatgtat----tacatatataacatatatgtattacatat -atgtaatacacatataatatatatgttatatatatatatatatataaaattttttaaaaa -attgtttcttgagatagggtctcactctgtcacccag ->ref_chr20:21721341-21721756 -tgtatatatatgtatgtatatatatatgtatatatgtatatatatatgtatataatacat -atatatacatatatattatatatgtaatacatatataatatatatgtaatgtatatatat -gtaatgtatataatatatatgtaatacatatataatatatatgtaatgtatat--tatat -atgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatattatatat -gtattacatatatgtattacatatataac-------atatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtaatacacatataatatatatgttatata -tatatatat--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------atataaaattttttaaaaa -attgtttcttgagatagggtctcactctgtcacccag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5b9c7d30d7119b8ee01d9d2df56da7df.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5b9c7d30d7119b8ee01d9d2df56da7df.msa deleted file mode 100644 index b1b3db87..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5b9c7d30d7119b8ee01d9d2df56da7df.msa +++ /dev/null @@ -1,120 +0,0 @@ ->syndip_1_chr20:35579913-35580986 -aaaactccatctcaaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga -ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct -gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca -ggcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatc -tgtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctac -tcaggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaa -gatttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtat -atacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaat -cccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagc -ctggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtgg -taacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacct -gggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgag -actctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatat -atatatatatatatatataatatatatatatataaaatatatatatataaaatatatata -tatataaaatatatatatataaaatatatatatatatataaaatatatatatataaaata -tatatatataaaatatatatatatataaaatatatatatatataaaatatatatatataa -aatatatatatatataaaatatatatatataaaatatatatatataaaatatatatatat -ataaaatatatatatataaaatatatatatataaaatatatatatatataatatatatat -ataaaatatatatatataaaatatatatataaaatatatatatataaaatatatatatat -aaaatatatatatataaaatatatatatataaaatatatatataaaatatatatatataa -aatatatatatataaaatatatatatataaaatatatatatggaattccatatctatcaa -tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagagga ->syndip_2_chr20:35579913-35580986 -aaaactccatctcaaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga -ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct -gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca -ggcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatc -tgtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctac -tcaggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaa -gatttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtat -atacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaat -cccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagc -ctggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtgg -taacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacct -gggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgag -actctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatat -at----------------------------------atatatatatataaa------ata -tatataatatatatatatata--------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------atatat -atat---------------aaaatatatataaaatatatatatataaaatatatatatat -aaaatatatatatataaaatat-------------------------------------- -----------------atatatatatataaaatatatatatggaattccatatctatcaa -tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagagga ->p:HG002_1_chr20:35579913-35580986 -aaaactccatctcaaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga -ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct -gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca -ggcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatc -tgtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctac -tcaggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaa -gatttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtat -atacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaat -cccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagc -ctggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtgg -taacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacct -gggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgag -actctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatat -at----------------------------------atatatatatataaa------ata -tatataatatatatatatata--------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------atatat -atat---------------aaaatatatataaaatatatatatataaaatatatatatat -aaaatatatatatataaaatat-------------------------------------- -----------------atatatatatataaaatatatatatggaattccatatctatcaa -tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagagga ->p:HG002_2_chr20:35579913-35580986 -aaaactccatctcaaaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga -ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct -gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca -ggcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatc -tgtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctac -tcaggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaa -gatttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtat -atacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaat -cccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagc -ctggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtgg -taacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacct -gggaggcacaggttgcagtgagccgagatcgtgccactgcagcctaggcagcagagtgag -actctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatat -atatatatatatatatataataaatatatatataaaatatatatatataaaatatatata -tatataaaatatatatatataaaatatatatatatatataaaatatatatatataaaata -tatatatataaaatatatatatatataaaatatatatatatataaaatatatatatataa -aatatatatatatataaaatatatatatataaaatatatatatataaaatatatatatat -ataaaatatatatatataaaatatatatatataaaatatatatatatataatatatatat -ataaaatatatatatataaaatatatatataaaatatatatatataaaatatatatatat -aaaatatatatatataaaatatatatatataaaatatatatataaaatatatatatataa -aatatatatatataaaatatatatatataaaatatatatatggaattccatatctatcaa -tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagagga ->ref_chr20:35579913-35580986 -aaaactccatctc-aaaaaaaaaaaaaaaaaaaaagggacacaatcctggattcaaaaga -ctgttgtaaatatcaaatgacataatagaaacataagtactttggagcctacaaagtgct -gtcagaagctgggcatggtggctcatgcctgtaaccccagcactttgggaggctgaggca -ggcagactgctcaaactcaggagttcgagaccagcctgggcaacatggcaagacaccatc -tgtaccaaaaatacaaaaaaatagccgggcatagtggtgcgcacctgtggtcccagctac -tcaggaggttgaggtgggaggatcacttgagcccagggggcggaggttacagtgagccaa -gatttgcactccagccttggtgacagagcaagagaccctgtctaaaatatatatgtgtat -atacacacacacacacacaaatatattttttggctgggcatggtggctgacacctgtaat -cccagcactttgggaggccaaggcaggcagatcacttgaggtcaggagtttgagaccagc -ctggccaagatgatgaaatcctgtctctactaaaaatacaaaaaaattagctgggtgtgg -taacgggtggctgtaatcccagctacttgggaagctgaggcagaagaatagcttgaacct -gggaggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgag -actctgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatat -at-------------------------atatataaaatatatatatataaa------ata -tatataaaatatatatatataaa------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------atatatatataatatatatat -ataa---------------aatatatatatataatatatatatataaaatatatatatat -aaaatatatatatatataaaat-------------------------------------- -----------------atatatatatataaaatatatatatggaattccatatctatcaa -tggatcctaagggaaacaattttactactgtattggtgggtttattttatgtatttgtag -atatatacatatatacacatatatatgacaattttagcacaaaagagagga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5c28c7bea0b0ee394555d0d2a8b5d2d4.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5c28c7bea0b0ee394555d0d2a8b5d2d4.msa deleted file mode 100644 index 607783f6..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5c28c7bea0b0ee394555d0d2a8b5d2d4.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:62349511-62350033 -cgaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcaga -caattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggagga -agcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggt -gatgatggtgatggtgggggtgatgatggtgatggtgatggtgatggtgggggtggtgat -ggtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgat -gacggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggaggg -gtgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggt -gggggtgggggtgatgacggtgat---------------------ggtgggggtgatgac -ggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgat -gacggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggt -gatgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtg -ggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacg -gtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg -gtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggta -gaggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgggggtg -atgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggg -gtggg------------------------------------------------------- --ggtgggggtgggggtgatgacggtgat-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------ggtgggggtgatgatggtgggagtgggctggtagt -gggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgct -ggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgca -gggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc ->syndip_2_chr20:62349511-62350033 -cgaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcaga -caattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggagga -agcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggt -gatgatggtgatggtgggggtgatgatggtgatggtga---------------tggtgat -ggtgatggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgat -gacggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggaggg -gtgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggt -gggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgac -ggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgat -gacggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggt -gatgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtg -ggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacg -gtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg -gtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggta -gaggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtg -atgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggg -gtgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatga -cggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtga -tgacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg -gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggggg -tgggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtggggg -tgggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtgg -gggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagt -gggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgct -ggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgca -gggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc ->p:HG002_1_chr20:62349511-62350033 -cgaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcaga -caattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggagga -agcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggt -gatgatggtgatggtgggggtgatgatggtgatggtga---------------tggtgat -ggtgatggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgat -gacggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggaggg -gtgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggt -gggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgac -ggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgat -gacggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggt -gatgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtg -ggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacg -gtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg -gtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggta -gaggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtg -atgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggg -gtgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatga -cggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtga -tgacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgg -gggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtggggg -tgggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtggggg -tgggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtgg -gggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagt -gggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgct -ggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgca -gggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc ->p:HG002_2_chr20:62349511-62350033 -cgaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcaga -caattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggagga -agcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggt -gatgatggtgatggtgggggtgatgatggtgatggtgatggtgatggtgggggtggtgat -ggtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgat -gacggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggaggg -gtgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggt -gggggtgggggtgatgacggtgat---------------------ggtgggggtgatgac -ggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgat -gacggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggt -gatgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtg -ggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacg -gtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtg -atgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggg -gtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggta -gaggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgggggtg -atgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtgggg -gtggg------------------------------------------------------- --ggtgggggtgggggtgatgacggtgat-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------ggtgggggtgatgatggtgggagtgggctggtagt -gggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgct -ggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgca -gggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc ->ref_chr20:62349511-62350033 -cgaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcaga -caattccggatagactgtcatggaatagaaaaactacagggtgcatttcag--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------gaaggaggaa -gcagcaacccaggggatggggatggggatggggatggtgggggtgatgggggtgatgatg -gtgatggtgatggtgatggtgatggtgatggtgatggtggg---------ggtggtgatg ------------ggtgggggtgatgacggtgggagtgggggtgatgacggtgatggtgggg -gtgat-----------------------------------------------------ga -cggtgatggtgggggtgatgacggtgat-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------ggtgggggtgatgatggtgggagtgggctggtagt -gggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgct -ggctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgca -gggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_5c809ebb257fbdb38f0a3a0d3ccb1af7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_5c809ebb257fbdb38f0a3a0d3ccb1af7.msa deleted file mode 100644 index 5bcf71fa..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_5c809ebb257fbdb38f0a3a0d3ccb1af7.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:13848162-13848654 -cctgggggacagagggaaattgcgtctcaaaaaaaaaaaagaagaagaaaagtagaagac -gaagatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagaga -aggagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaagaagaaga -agaagaagaagaagaagaagaagaagaagaagaagaagaagtcaaata---tctggagaa -gaagaagaagaggaagaagaagaaaaggaagaagaagaagaagaggaagaggaagaaaga -agaagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaa -gaagaagaagaggaggaggaagaaggagaaggagaagaagaagaagaagcaggagcagga -gaagaagaagaagaagaagaagaagaggaagaggaagaggaagagggagaaggagaagga -gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaaaatacaaatatctggagccgggatttgagcctggc ->syndip_2_chr20:13848162-13848654 -cctgggggacagagggaaattgcgtctcaaaaaaaaaaaagaagaagaaaagtagaagac -gaagatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagaga -aggagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaagaagaaga -agaagaagaagaagaagaagaagaagaagaagaagaagaagtcaaata---tctggagaa -gaagaagaagaggaagaagaagaaaaggaagaagaagaagaagaggaagaggaagaaaga -agaagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaa -gaagaagaagaggaggaggaagaaggagaaggagaaggagaaggagaaggaggagcagga -gaagaagaagaagaagaagaagaagaggaagaggaagaggaagag--------------- -gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaaaatacaaatatctggagccgggatttgagcctggc ->p:HG002_1_chr20:13848162-13848654 -cctgggggacagagggaaattgcgtctcaaaaaaaaaaaagaagaagaaaagtagaagac -gaagatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagaga -a-gagaaggagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaaga -agaagaagaagaagaagtcaaataagaagaagaagaagaagtcaaatatcttctggagaa -gaagaagaagaggaagaagaagaaaaggaagaagaagaagaagaggaagaggaagaaaga -agaagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaa -gaagaagaagaggaggaggaagaaggagaaggagaaggagaaggagaaggaggagcagga -gaagaagaagaagaagaagaagaagaggaagaggaagaggaagag--------------- -gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaaaatacaaatatctggagccgggatttgagcctggc ->p:HG002_2_chr20:13848162-13848654 -cctgggggacagagggaaattgcgtctcaaaaaaaaaaaagaagaagaaaagtagaagac -gaagatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagaga -a-gagaaggagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaaga -agaagaagaagaagaagtcaaataagaagaagaagaagaagtcaaatatcttctggagaa -gaagaagaagaggaagaagaagaaaaggaagaagaagaagaagaggaagaggaagaaaga -agaagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaa -gaagaagaagaggaggaggaagaaggagaaggagaagaagaagaagaagcaggagcagga -gaagaagaagaagaagaagaagaagaggaagaggaagaggaagagggagaaggagaagga -gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaaaatacaaatatctggagccgggatttgagcctggc ->ref_chr20:13848162-13848654 -cctgggggacagagggaaattgcgtctcaaaaaaaaaaaagaagaagaaaagtagaagac -gaagatgaagaagaataagaagagagaaaagaagaagagaaggttagagaaaagaagaga -a-gagaaggagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaagaaga -agaagaagaagaagaagtcaaata---------------------------tctggagaa -gaagaagaagaggaagaagaagaaaaggaagaagaagaagaagaggaagaggaagaaaga -agaagaacaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaa -gaagaagaagaggaggaggaagaaggagaaggagaaggagaaggagaagga--------- ------------------------------------------------------------- -gaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaaaatacaaatatctggagccgggatttgagcctggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_610225dfecd33128cb4715dc4a0d63ae.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_610225dfecd33128cb4715dc4a0d63ae.msa deleted file mode 100644 index 1e1c440a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_610225dfecd33128cb4715dc4a0d63ae.msa +++ /dev/null @@ -1,130 +0,0 @@ ->syndip_1_chr20:63028775-63029503 -tcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggct -gagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcc -aaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctcc -gcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcct -ccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggc -ctccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc -gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtccc -ccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtc -ccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcagg -tcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtg -tgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtg -tgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctc -cgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagttt -gccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaat -tcatttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattc -at ->syndip_2_chr20:63028775-63029503 -tcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggct -gagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcc -aaa--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------cgca -cccga------------------------------------------------------- ------------------------------------------------------------- ----------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctc -cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagttt -gccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaat -tcatttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattc -at ->p:HG002_1_chr20:63028775-63029503 -tcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggct -gagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcc -aaa--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------cgca -cccga------------------------------------------------------- ------------------------------------------------------------- ----------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctc -cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagttt -gccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaat -tcatttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattc -at ->p:HG002_2_chr20:63028775-63029503 -tcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggct -gagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcc -aaacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctcc -gcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcct -ccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggc -ctccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgcgtgtgcaggtcccccgg -gcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtccccc -gggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtccc -ccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtc -ccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcagg -tcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtg -tgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtg -tgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctc -cgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagttt -gccaacgtccatgcacgtctcagcctctcagcctggactggacaactcggcttcgggaat -tcatttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgaattc -at ->ref_chr20:63028775-63029503 -tcaacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggct -gagcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcc -aaa--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------cgca -cccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc -cgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgtctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagttt -gccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaat -tcatttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattc -at diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6119bd2cffedc02e25f7f14d616217a8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6119bd2cffedc02e25f7f14d616217a8.msa deleted file mode 100644 index 3bf2163c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6119bd2cffedc02e25f7f14d616217a8.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:34235788-34236091 -agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaa -ggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaggaagcg -ggagggagggaagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaagga -aggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagg -gagggaagaaggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaag -agagaaagagagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagag -aaagaaagagaaagagaaggaagga ->syndip_2_chr20:34235788-34236091 -agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaa -ggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaggaagcg -ggagggagggaagaaggaaggaaggaggagggagggaagaatgaaggaaggaaggaagga -aggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagg -gagggaagaaggaaggaggagggagggagggaagcaggaaagaaggaaggaaggagaaag -agagaaagagagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagag -aaagaaagagaaagagaaggaagga ->p:HG002_1_chr20:34235788-34236091 -agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaa -ggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaaggaa-g -gaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaagga -gggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagg -gagggaagaaggaaggaggagggagggagggaagaaggaaagaaggaaggaaggagaaag -agagaaagagagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagag -aaagaaagagaaagagaaggaagga ->p:HG002_2_chr20:34235788-34236091 -agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaa -ggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaaggaa-g -gaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaagga -gggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagg -gagggaagaaggaaggaggagggagggagggaagaaggaaagaaggaaggaaggagaaag -agagaaagagagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagag -aaagaaagagaaagagaaggaagga ->ref_chr20:34235788-34236091 -agaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaggaa -ggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaaggaaggaaggaaaggaa-- ------------------------------------------------------ggaagga -aggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaaggaaggagggagg -gagggaaga--------------------------aggaaagaaggaaggaaggagaaag -agagaaagagagagagaagaagaaagagaaagaaacagaaaaggaaggaaggagagagag -aaagaaagagaaagagaaggaagga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6125f7292d70d0bf730d50e79d9e5f9d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6125f7292d70d0bf730d50e79d9e5f9d.msa deleted file mode 100644 index a524e701..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6125f7292d70d0bf730d50e79d9e5f9d.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:63559188-63560063 -tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc -aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct -gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt -ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt -caggtgggag----------------------------------------tcagtcaggg -tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcaggt---cggagtcagggtcaggtgggaggagtcagg -gtcaggtgggagtcagtcagggtcaggtgggagg-------------------------- -----------------------------------------------------agtcaggg -tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc -aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa -gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac -attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggac ->syndip_2_chr20:63559188-63560063 -tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc -aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct -gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt -ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga----------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------ggagtcagggtcaggtgggaggagtcagg -gtcaggtgggagtc---------------------------------------------- -----------------------------------------------------agtcaggg -tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagg -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc -aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa -gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac -attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggac ->p:HG002_1_chr20:63559188-63560063 -tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc -aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct -gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt -ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga----------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------ggagtcagggtcaggtgggaggagtcagg -gtcaggtgggagtc---------------------------------------------- -----------------------------------------------------agtcaggg -tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcagg -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc -aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa -gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac -gttcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggac ->p:HG002_2_chr20:63559188-63560063 -tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc -aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct -gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt -ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt -caggtgggag----------------------------------------tcagtcaggg -tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcaggt---cggagtcagggtcaggtgggaggagtcagg -gtcaggtgggagtcagtcagggtcaggtgggagg-------------------------- -----------------------------------------------------agtcaggg -tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc -aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa -gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac -gttcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggac ->ref_chr20:63559188-63560063 -tgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctcttc -aggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgct -gagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtggt -ctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcagggt -caggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcaggg -tcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcagg -gtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtcag -ggtcaggtcggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtcaggg -tcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcaga -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggtc -aggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctggaa -gagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagccac -attcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtggg -ccgctggtccaggtcgctcttggcacaggtgcggac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_615dccf03cc31e876bed1aad360c151d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_615dccf03cc31e876bed1aad360c151d.msa deleted file mode 100644 index fb00fce1..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_615dccf03cc31e876bed1aad360c151d.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:61201582-61202575 -aaatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctat -actactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtt -agagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggac -cctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcctta -ctcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacct -ccatcctcactcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg- -gtgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggat -cccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc-- ---ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtca -cctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca----- ------------------------ccaggaccctccatgagtgtcacctccatcctcactc -aggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctcca -tcctcactcaggaccctccat-ggtgtcaccgccatcctca------------------- -------------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagg -atcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcc -tcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtca -cctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctcca -tgagtgtcacctccatcctca--------------------------ctcaggaccctcc -atg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactca -ggaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctcca -tcctcactcaggaccctccatg-gtgtcacctccatcctcaccaggaccctccatgagtg -tcacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccc -tccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcact -caggaccctccatg-----------------------------------gtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcaccaggaccctccatgagtg -tcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccct -ccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccc -tcaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgtt -tcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttggg -cacctctctctcagactaggct ->syndip_2_chr20:61201582-61202575 -aaatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctat -actactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatt -agagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggac -cctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcctta -ctcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgggtgtcacct -ccatcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatga -gtgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcagga -ccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcct -cactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtca -cctccatcctcactcaggaccctccatgggtgccacctccatcctcaccaggatcccctg -taagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggacc -ctccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactc -aggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctcca -tcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagt -gtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag -gaccctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcc -ttactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgcca -cctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctcca -tgagtgtcacctccatcctcaggaccctccatggtgtcacctccatcctcaggaccctcc -atgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactca -ggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctcca -tcctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggacac -tccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcact -caggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccct -ccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccc -taaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgtt -tcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttggg -cacctctctctcagactaggct ->p:HG002_1_chr20:61201582-61202575 -aaatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctat -actactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatt -agagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggac -cctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcctta -ctcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgggtgtcacct -ccatcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatga -gtgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcagga -ccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcct -cactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtca -cctccatcctcactcaggaccctccatgggtgccacctccatcctcaccaggatcccctg -taagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggacc -ctccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactc -aggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctcca -tcctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagt -gtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag -gaccctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcc -ttactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgcca -cctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctcca -tgagtgtcacctccatcctcaggaccctccatggtgtcacctccatcctcaggaccctcc -atgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactca -ggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctcca -tcctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggacac -tccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcact -caggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccct -ccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccc -taaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgtt -tcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttggg -cacctctctctcagactaggct ->p:HG002_2_chr20:61201582-61202575 -aaatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctat -actactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtt -agagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggac -cctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcctta -ctcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacct -ccatcctcactcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg- -gtgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggat -cccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc-- ---ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtca -cctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca----- ------------------------ccaggaccctccatgagtgtcacctccatcctcactc -aggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctcca -tcctcactcaggaccctccat-ggtgtcaccgccatcctca------------------- -------------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagg -atcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcc -tcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtca -cctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctcca -tgagtgtcacctccatcctca--------------------------ctcaggaccctcc -atg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactca -ggaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctcca -tcctcactcaggaccctccatg-gtgtcacctccatcctcaccaggaccctccatgagtg -tcacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccc -tccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcact -caggaccctccatg-----------------------------------gtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcaccaggaccctccatgagtg -tcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccct -ccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccc -tcaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgtt -tcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttggg -cacctctctctcagactaggct ->ref_chr20:61201582-61202575 -aaatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctat -actactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatt -agagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggac -cctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcctta -ctcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacct -ccatcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatga -gtgtcacctccatcct-------------------------------------------- ------------------------------caggaccctccatgagtgtcacctccatcct -cactcaggaccctccat------------------------------------ggtgtca -ccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcccctg -taa--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------gtgtcacctccatcctcaccaggaccctccatgagtg -tcacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccc -tccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcact -caggaccctccatg----------------------------------ggtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccct -ccgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccc -tcaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgtt -tcagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttggg -cacctctctctcagactaggct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_616ca6c0f370a4f30d5061d4f8f648de.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_616ca6c0f370a4f30d5061d4f8f648de.msa deleted file mode 100644 index 2fa0c760..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_616ca6c0f370a4f30d5061d4f8f648de.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:59384256-59384853 -gtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcagggaggaggtaga -ggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcgggggaaggaggtga -tggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggggaggatgtgggg -gaggtggggagcaaggaggtgatggggaggaggtgagtggggagg--------------- -----------------------------------------------tggtgagcagggag -gaggtgagggggcaagggaggtgatggggaggaaggaggttatggggaggtggtgagtg- --------------gggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtggg -gaggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgg -ggaggaaggtggggggaaggaggtgatagggaggatgtgggggaggtgggggggaaggag -gtgaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtga -gtggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcggaggaagga -ggtgatgggaaggaggtgagtgtgtaggaggtaag-----cagggaggaagtggggagga -aggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaa -ggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaag -gaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaagg -aggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaagga -ggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggag -gtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga ->syndip_2_chr20:59384256-59384853 -gtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcagggaggaggtaga -ggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcgggggaaggaggtga -tggggaggaggtgagtggggaggaaggtgggaggaaggaggtgatggggaggatgtgggg -gaggtggggagcaaggaggtgatggggaggaggtgagtggggaggtggtgagcagggagg -aggtgagggggcaagggaggtgatggggaggaggtgagtggggaggtggtgagcggggag -gaggtgagggggcaagggaggtgatggggaggaaggaggttatggggaggtggtgagtg- --------------gggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtggg -gaggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgg -ggaggaaggtggggggaaggaggtgatagggaggatgtgggggaggtgggggggaaggag -gtgaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtga -gtggggaagtggtgagaggggag------------------------------------- ----------------------------gaggtgagggggcaagggaggcgatgcggagga -aggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaa -ggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaag -gaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga-------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------- ->p:HG002_1_chr20:59384256-59384853 -gtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcagggaggaggtaga -ggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcgggggaaggaggtga -tggggaggaggtgagtggggaggaaggtggggggaaggaggtgatagggaggatgtgggg -gaggtgggggggaaggaggtgaggcagaggaggggagtggggagg--------------- -----gagatgagtaaggaagtgatggggagagggtgagtggggaagtggtgagaggggag -gaggtgagggggcaagggaggcgatgcggaggaaggaggtgatgggaaggaggtgagtgt -gtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggaggaggtgagtgtg -taggaggtaagcagggaggaagtgggggggcaagggaggtgatggggaggaggtgagtgg -ggaggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggag -gtgaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtga -gtggggaagtggtgagaggggag------------------------------------- ----------------------------gaggtgagggggcaagggaggcgatgcggagga -aggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaa -ggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaag -gaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga-------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------- ->p:HG002_2_chr20:59384256-59384853 -gtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcagggaggaggtaga -ggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcgggggaaggaggtga -tggggaggaggtgagtggggaggaaggtggggggaaggaggtgatagggaggatgtgggg -gaggtgggggggaaggaggtgaggcagaggaggggagtggggagg--------------- -----------------------------------------------tggtgagcagggag -gaggtgagggggcaagggaggtgatggggaggaaggaggttatggggaggtggtgagtg- --------------gggagggaggtaaggggtaaggtggtgatgtggaggtggtgagtggg -gaggtggtgagaggggaggagatgagggggcaagggaggtgatggggaggaggtgagtgg -ggaggaaggtggggggaaggaggtgatggggaggatgtgggggaggtgggggggaaggag -gtgaggcagaggaggggagtggggagggagatgagtaaggaagtgatggggagagggtga -gtggggaagtggtgagaggggag-----gaggagatgagtaaggaagtgatggggagagg -gtgagtggggaagtggtgagaggggaggaggtgagggggcaagggaggcgatgcggagga -aggaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaa -ggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaag -gaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaagg -aggtgatgggaaggaggtgagtgtgtaggaggtaagcagggaggaagtggggaggaagga -ggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaaggag -gtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga ->ref_chr20:59384256-59384853 -gtgataggaggtgagtgggcaggaggtgagcagggaggaggcgagcagggaggaggtaga -ggggaaggaagtgatggggaggaggtgaggggggaaagaggtggcgggggaaggaggtga -tggggaggaggtgagtggggaggaaggtggggggaaggaggtgatagggaggatgtgggg -gaggtgggggggaaggaggtgaggcagaggaggggagtggggagg--------------- -----gagatgagtaaggaagtgatggggagagggtgagtggggaagtggtgagaggggag -gaggtgagggggcaagggaggcgatgcggaggaaggaggtgatgggaaggaggtgagtgt -gtaggaggtaagcagggaggaagtgggggggaaggaggtgatggggaggaggtgagtgtg -taggaggtaagcagggaggaagtggggg-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------gga -aggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaa -ggaggtgatggggaggaggtgagtgtgtaggaggtaagcagggaggaagtgggggggaag -gaggtgatgggaaggaggtgagtgtgtaggaggtaagcagggagga-------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6272ac8c11659a343276a77a33bea482.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6272ac8c11659a343276a77a33bea482.msa deleted file mode 100644 index 080f1729..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6272ac8c11659a343276a77a33bea482.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:21721074-21721835 -agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt -cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag -accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat -attatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatatat -attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat -atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata -tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat -aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat -attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat -tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtaatacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtaatacatatataacatatatgta -ttacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatataa -catatatgtattacatatatgtaatacatatataac----atgtattacatatatgtaat -acatatataac--------------------------atgtattacatatatgtaataca -tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat -atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc -tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcc ->syndip_2_chr20:21721074-21721835 -agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt -cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag -accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat -attatatatgtaatgtatataatatatgtaatgtatataatacatatgtaatacatatat -attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat -atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata -tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat -aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat -attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat -tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaat -acatatataacatatatgtaatacatatataacatatatgtattacatatatgtaataca -tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat -atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc -tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcc ->p:HG002_1_chr20:21721074-21721835 -agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt -cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag -accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat -attatatatgtaatgtatataatatatgtaatgtatataatacatatgtaatacatatat -attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat -atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata -tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat -aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat -attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat -tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtattacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtattacatatataacatatatgta -ttacatatatgtattacatatataacatatatgtattacatatatgtattacatatataa -catatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaat -acatatataacatatatgtaatacatatataacatatatgtattacatatatgtaataca -tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat -atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc -tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcc ->p:HG002_2_chr20:21721074-21721835 -agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt -cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag -accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat -attatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatatat -attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat -atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata -tataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatatat -aatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat -attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat -tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtattacatatataacatatatgtattaca -tatatgtattacatatataacatatatgtaatacatatatgtattacatatataacatat -atgtattacatatatgtattacatatataacatatatgtattacatatatgtattacata -tataacatatatgtattacatatatgtattacatatataacatatatgtattacatatat -gtattacatatataacatatatgtattacatatatgtaatacatatataacatatatgta -ttacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatataa -catatatgtattacatatatgtaatacatatataac----atgtattacatatatgtaat -acatatataac--------------------------atgtattacatatatgtaataca -tatataacatgtattacatatatgtaatacacatataatatatatgttatatatatatat -atatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc -tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcc ->ref_chr20:21721074-21721835 -agtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgtttt -cttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgtag -accacattggctattacatatatatatataatatatatgtaatatatatatgtaatgtat -attatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatatat -attatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtatat -atgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacata -tataatatatatgtaatgt----------------------------------------- --atatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgtat -attatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtatat -tatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtatt -acatatataacatatatgtattacatatatgtaatacacatataatatatatgttatata -tatatatat--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---atataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccaggc -tggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgatc -ctcccacctcaacctcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_632c129ea66080082af1456d555cccb9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_632c129ea66080082af1456d555cccb9.msa deleted file mode 100644 index fa82a1b9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_632c129ea66080082af1456d555cccb9.msa +++ /dev/null @@ -1,640 +0,0 @@ ->syndip_1_chr20:63693339-63693842 -cagagtcctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgt -tcccctatgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctcc -accttcaccaccaccacctccaccaccacctccaccacctccacctccaccacctccacc -acctccaccaccaccacctccaccaccaccacctccaccaccaccaccaccaccacctcc -accaccaccaccaccaccaccacctccacctccaccacctccaccaccacctccacctcc -accaccacctccacctccacctccaccaccaccacctccaccacctccaccacctccacc -tccaccaccacctccacctccaccaccacctccacctccacctccacctccacctccacc -accaccacctccaccacctccaccacctccacctccaccaccaccacctccacctccacc -tccaccacctccacctccaccacctccacctccaccacctccaccaccaccaccaccacc -accaccacctccaccaccaccaccaccaccacctccaccacctccacctccaccacctcc -accaccaccacctccaccaccacctccaccaccacctccacctccaccacctccacctcc -accacctccacctccacctccaccaccacctccaccacctccaccaccacctccaccacc -tccacctccaccaccaccacctccaccaccaccaccaccaccacctccaccacctccacc -tccaccacctccaccaccaccacctccaccaccacctccaccaccacctccacctccacc -acctccacctccaccacctccacctccacctccaccaccacctccaccacctccaccacc -acctccaccacctccaccacctccaccaccacctccaccacctccacctccaccaccacc -acctccacctccaccaccaccacctccaccaccacctccacctccaccaccaccacctcc -acctccaccaccaccacctccaccaccacctccaccaccaccaccaccaccaccacctcc -acctccaccacctccaccaccaccaccaccacctccacctccaccacctccaccacctcc -accaccaccaccaccacctccaccacctccaccaccacctccaccacctccacctccacc -accaccacctccaccaccaccacctccacctccacctccacctccacctccaccaccacc -tccacctccaccaccacctccaccaccacctccacctccaccacctccacctccacctcc -accacctccaccaccaccaccaccaccaccaccaccaccaccacctccaccacctccacc -tccacctccaccaccaccaccaccacctccaccaccaccaccaccacctccaccacctcc -accaccacctccaccaccaccaccaccaccaccaccaccacctccaccacctccacctcc -acctccacctccaccacctccaccacctccaccaccacctccaccaccaccaccaccacc -tccaccaccacctccacctccaccaccacctccaccaccacctccacctccaccacctcc -acctccaccacctccaccacctccacctccaccacctccacctccacctccaccacctcc -accaccaccaccaccaccaccaccaccaccaccacctccaccaccaccacctccaccacc -acctccaccacctccaccaccacctccaccaccaccaccaccaccaccaccaccaccacc -acctccaccaccacctccacctccaccaccacctccaccaccacctccacctccaccacc -tccacctccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctcc -acctccaccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctcc -accacctccaccaccacctccacctccaccacctccaccaccacctccaccaccacctcc -accaccaccacctccaccaccacctccaccacctccaccaccacctccacctccaccacc -tccaccaccacctccaccaccacctccaccaccaccacctccaccaccacctccaccacc -tccaccaccacctccacctccaccacctccacctccacctccaccacctccaccaccacc -accaccaccaccaccaccaccaccaccaccaccaccaccacctccacctccacctccacc -acctccacctccaccacctccaccaccacctccacctccaccacctccacctccacctcc -accacctccacctccaccacctccacctccacctccaccacctccaccaccaccacctcc -accaccacctccaccacctccaccaccacctccacctccaccacctccaccaccacctcc -accaccacctccaccaccaccacctccaccaccacctccaccacctccaccaccacctcc -acctccaccacctccacctccacctccaccacctccaccaccaccaccaccaccaccacc -accaccaccacctccaccaccaccacctccaccaccacctccaccaccaccaccaccacc -tccaccaccaccaccaccacctccaccaccacctccaccacctccaccaccaccaccacc -accaccaccacctccaccaccacctccaccaccaccaccaccaccaccaccacctccacc -acctccacctccaccaccaccaccacctccaccaccacca------------------cc -accaccacctccacctccaccaccaccacctccaccaccaccaccacctccaccaccacc -tccaccaccaccaccaccaccaccaccaccacctccaccacctccaccacctccaccacc -acctccaccacctccaccaccaccaccaccacctccaccaccacctccaccaccaccacc -accaccaccacctccacctccacctccaccacctccacctccaccacctccacctccacc -acctccacctccacct---ccacctccaccaccacctccacctccaccaccacctcctcc -accaccaccacctccaccaccaccaccaccaccaccacctccacctccaccacctccacc -tccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccacctcc -accacctccacctccaccaccaccacctccaccaccaccacctccacctccaccaccacc -accaccaccacctccacctccaccaccacctccaccaccacctccacctccacctccacc -acctccaccaccacctccaccacctccaccacctccacctccaccaccaccaccacctcc -accaccaccaccaccacctctaccacctctaccaccaccaccaccacctccaccaccacc -accaccacctccaccaccaccaccaccaccacctccaccaccacctccaccacctccacc -accaccaccaccacctctaccacctccacctccaccaccaccaccacctctaccaccacc -accaccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctcc -accaccacctccaccacctccaccaccaccaccacctccacctccaccacctccaccacc -acctccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccaccacc -accaccacctctaccacctccacctccaccaccaccaccacctccacctccaccaccacc -accaccaccaccaccaccaccacctccaccaccaccaccaccaccacctctaccaccacc -accaccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctcc -accaccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccacc -accacctccaccaccaccaccacctccaccaccacctccaccaccaccaccacctccacc -accacctccaccaccacctccaccacctccaccaccaccaccaccacctccaccaccacc -tccacctccaccaccaccaccaccacctccaccaccaccaccaccaccaccacctccacc -accacctccaccaccacctccaccacctccaccaccaccaccaccacctccaccaccacc -tccacctccaccaccaccaccaccacctccaccaccacctccaccaccaccaccaccacc -acctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctctacc -accaccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccaccacc -accacctccacctccaccaccaccacctccaccacctccaccaccacctccaccaccacc -acctccacctccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccacc -acctccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccaccacc -accaccacctctaccacctctaccaccaccaccaccacctccaccaccaccaccacctcc -accaccaccaccacctccaccaccacctccaccaccaccacctccacctccaccaccacc -acctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccacc -tccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccaccacc -tccaccaccaccacctccaccacctccaccaccaccaccaccacctccaccacctccacc -acctccaccaccaccaccaccacctccacctccacctccaccacctccaccaccaccacc -tccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctccacctcc -accaccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctcc -accaccaccacctccaccaccaccacctccacctccaccacctccaccaccacctccacc -accaccacctccacctccaccaccaccacctccaccaccaccacctccacctccaccacc -accacctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccacc -acctccaccacctccaccaccaccacctccaccaccaccacctccaccacctccaccacc -accaccaccacctccaccacctccaccacctccaccaccaccaccaccacctccacctcc -acctccaccacctccaccaccaccacctccaccaccaccaccaccaccacctccaccacc -tccaccaccaccaccaccacctccacctccacctccaccacctccaccaccaccacctcc -accaccaccaccaccaccaccaccaccacctccacctccacctccaccacctccacctcc 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-accaccaccaccaccaccaccacctccaccaccaccaccaccaccacctctaccaccacc -accaccacctccaccaccaccaccacctccaccaccaccaccacctccaccaccacctcc -accaccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccacc -accacctccaccaccaccaccacctccaccaccacctccaccaccaccaccacctccacc -accacctccaccaccacctccaccacctccaccaccaccaccaccacctccaccaccacc -tccacctccaccaccaccaccaccacctccaccaccaccaccaccaccaccacctccacc -accacctccaccaccacctccaccacctccaccaccaccaccaccacctccaccaccacc -tccacctccaccaccaccaccaccacctccaccaccacctccaccaccaccaccaccacc -acctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctctacc -accaccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccaccacc -accacctccacctccaccaccaccacctccaccacctccaccaccacctccaccaccacc -acctccacctccaccaccaccacctccaccacctccaccaccaccaccaccaccaccacc -acctccaccaccaccaccaccaccacctccaccaccacctccaccacctccaccaccacc -accaccacctctaccacctctaccaccaccaccaccacctccaccaccaccaccacctcc -accaccaccaccacctccaccaccacctccaccaccaccacctccacctccaccaccacc -acctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccacc -tccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccaccacc -tccaccaccaccacctccaccacctccaccaccaccaccaccacctccaccacctccacc -acctccaccaccaccaccaccacctccacctccacctccaccacctccaccaccaccacc -tccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctccacctcc -accaccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctcc -accaccaccacctccaccaccaccacctccacctccaccacctccaccaccacctccacc -accaccacctccacctccaccaccaccacctccaccaccaccacctccacctccaccacc -accacctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccacc -acctccaccacctccaccaccaccacctccaccaccaccacctccaccacctccaccacc -accaccaccacctccaccacctccaccacctccaccaccaccaccaccacctccacctcc -acctccaccacctccaccaccaccacctccaccaccaccaccaccaccacctccaccacc -tccaccaccaccaccaccacctccacctccacctccaccacctccaccaccaccacctcc -accaccaccaccaccaccaccaccaccacctccacctccacctccaccacctccacctcc -accaccaccaccaccaccaccacctccaccaccacctccacctccacctccaccacctcc -acctccaccaccaccaccaccaccaccaccaccaccaccacctccacctccacctccacc -accaccacctctaccaccacctccaccaccaccaccaccaccaccaccaccacctccacc -acctccaccaccaccacctccaccaccaccacctccacctccaccaccaccaccacctcc -accacctccaccaccacctccacctccacctccaccacctccaccaccaccacctccacc -accaccaccaccaccaccacctccaccacctccaccaccaccacctccaccaccaccacc -tccacctccaccacctccaccacctccaccaccaccaccacctccaccaccaccaccacc -accacctccacctccaccacctctaccaccacctccaccaccaccaccaccaccacctcc -acctccaccacctccacctccaccacctctaccaccacctccaccaccaccacctccacc -tccacctccaccaccaccacctccacctccacctccaccaccaccaccaccaccaccacc -tccaccaccaccaccaccaccaccaccaccacctccacctccaccaccaccacctccacc -accaccacctccaccacctccaccaccacctccacctccaccaccaccacctccacctcc -acctccaccaccaccaccaccacctccaccaccaccacctccaccaccaacacctccacc -tccacctccaccaccaccaccaccacctccacctccaccaccacctccaccaccaccacc -tccacctccaccaccaccacctccaccaccacctccaccacctccaccaccaccacctcc -accaccacctccaccaccaccaccaccaccacctccacctccacctccaccaccaccacc -tctaccaccacctccaccaccaccaccaccaccaccaccaccacctccacctccacctcc -accacctccacctccaccaccaccaccaccaccaccacctccaccaccacctccacctcc -acctccaccacctccacctccaccaccaccaccaccaccaccaccaccaccaccacctcc -acctccacctccaccaccaccacctctaccaccacctccaccaccaccaccaccaccacc -accaccacctccaccaccaccacctccacctccaccaccaccacctccacctccaccacc -accacctccacctccaccaccaccaccaccaccaccacctccaccaccaccacctccacc -acctccaccaccacctccaccaccaccacctccaccacctccaccaccacctccacctcc -accaccaccacctccaccaccaccacctccacctccaccaccaccacctccacctccacc -tccaccacctccacctccaccacctccaccaccaccacctccaccacctccaccaccacc -tccacctccaccaccaccacctccaccaccaccacctccaccacctccaccaccacctcc -acctccaccaccaccacctccacctccacctccaccaccaccaccaccacctccactacc -accacctccacctccaccaccaccacctccaccaccaacacctccacctccacctccacc -tccaccaccaccacctccacctccaccaccaccacctccaccaccaccacctccaccacc -tccacctccaccaccaccacctccaccaccacctccaccaccaccaccacctccaccacc -acctccacctccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccacc -acctccaccaccaccacctgcaccaccacctccacctccaccaccaccaccacctccacc -tccaccagcagcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgt -ccctgccatagccccgacccc ->ref_chr20:63693339-63693842 -cagagtcctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgt -tcccctatgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctcc -acctccacctccacctccacctccaccaccacctccacctccaccaccacctcctccacc -acc--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------accacctccaccaccaccaccaccaccaccacctcc -acctccaccacctccacctccaccaccaccacct-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------ccacctccaccaccacc--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----acctccacctccaccaccacctccaccaccaccacctccacct-------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------ccaccaccacctcca-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------ccaccaccaccaccaccaccaccaccaccaccacc -acctccaccaccaccacctgcaccaccacctccacctccaccaccaccaccacctccacc -tccaccagcagcagcatcacttgttggggagaccctgtgcaactccatgcacagccctgt -ccctgccatagccccgacccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_65acc2ac17488729265ee87d68bd115b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_65acc2ac17488729265ee87d68bd115b.msa deleted file mode 100644 index d480a3c6..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_65acc2ac17488729265ee87d68bd115b.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:62270178-62271195 -ccgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtc -agctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcac -ctcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctct -gggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctg -ggtcctctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctcc -ttgtc-----------------------------cctctctgggtcctctccttgtccct -ctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgg -gtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctt -tccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgc -ctctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagc -tgtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa ->syndip_2_chr20:62270178-62271195 -ccgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtc -agctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcac -ctcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctct -gggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctc-ctgg-----------------------cctctctgggtcctctcc -ttgtc------------------------------------------------------- -----------------------------------------------------cctctctg -ggtcctctccttgtccctctctgacctctctgggtcctctccttgtccctctctgggtcc -tctccttgtc-----------------------------------------cctctctgg -gtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctt -tccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgc -ctctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagc -tgtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa ->p:HG002_1_chr20:62270178-62271195 -ccgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtc -agctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcac -ctcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctct -gggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctc-ctgg-----------------------cctctctgggtcctctcc -ttgtc------------------------------------------------------- -----------------------------------------------------cctctctg -ggtcctctccttgtccctctctgacctctctgggtcctctccttgtccctctctgggtcc -tctccttgtc-----------------------------------------cctctctgg -gtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctt -tccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgc -ctctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagc -tgtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa ->p:HG002_2_chr20:62270178-62271195 -ccgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtc -agctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcac -ctcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctct -gggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctg -ggtcctctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctcc -ttgtc-----------------------------cctctctgggtcctctccttgtccct -ctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgg -gtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctt -tccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgc -ctctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagc -tgtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgagaa ->ref_chr20:62270178-62271195 -ccgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtc -agctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcac -ctcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctct -gggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcct -ctctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctctgacctctctgggtcctctccttgtccct -ctctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgg -gtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcctt -tccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgc -ctctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagc -tgtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgggaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_66112df94acfa8f42760b311b37ff111.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_66112df94acfa8f42760b311b37ff111.msa deleted file mode 100644 index 4d2cea0e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_66112df94acfa8f42760b311b37ff111.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:57350708-57351087 -aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc -ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta -tttttagtactgacggggggacggggggacgggggacgggggacggggggcgggggggac -gggggacggggggcggggggggcgggggggacggggggcggggggg-gcgggggccgggg -ggggcggggggacgggggcggggggccggggggggcggggggacgggggcgggggggcgg -ggggggcggggggacgggggcggggggcgcgggggggcggggggggcggcgcgggggggc -gggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga -ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataa ->syndip_2_chr20:57350708-57351087 -aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc -ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta -tttttagtactgacggggggacgggggggc------------------------------ -------------------------gggggggcgggggggcgggggg-acggggggcgggg -ggggcggggggacgggggcggggggcgggggggggc------------------------ --------------------------ggcgcgggggggc---------------------- --ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga -ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataa ->p:HG002_1_chr20:57350708-57351087 -aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc -ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta -tttttagtactgacggggggacgggggggc------------------------------ -------------------------gggggggcgggggggcgggggg-acggggggcgggg -ggggcggggggacgggggcggggggcgggggggggc------------------------ --------------------------ggcgcgggggggc---------------------- --ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga -ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataa ->p:HG002_2_chr20:57350708-57351087 -aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc -ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta -tttttagtactgacggggggacggggggacgggggacgggggacggggggcgggggggac -gggggacggggggcggggggggcgggggggacggggggcggggggg-gcgggggccgggg -ggggcggggggacgggggcggggggccggggggggcggggggacgggggcgggggggcgg -ggggggcggggggacgggggcggggggcgcgggggggcggggggggcggcgcgggggggc -gggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga -ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataa ->ref_chr20:57350708-57351087 -aatggcatggtctcggctcactgcaacctccacctcctgggttcaagcgattctcctgcc -ttagcctcccaagcagctgggattacaggcacccgccaccatgcccggctaatttttgta -tttttagtactgacggggggacgggggggc------------------------------ -------------------------gggggggcggggggacggggggcggggggggcgggg -ggggcggggggacgggggcggggggcgggggggggc------------------------ --------------------------ggcgcgggggggc---------------------- --ggggggggcggggggcggggcggttcacgatgttggccagacttgtcttgaactcctga -ccccaggtgatcagcccgcctcggcctcccaaagtgctgggattacaggcgtgagccacc -gcgcctggccagttgcggatttataa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_673f5d4f5e6f63e7fa0ef8d5ce17997d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_673f5d4f5e6f63e7fa0ef8d5ce17997d.msa deleted file mode 100644 index e171204c..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_673f5d4f5e6f63e7fa0ef8d5ce17997d.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:63641737-63642125 -gctgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgc -ctcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcc -cagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccg -agctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgccc -cccgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgccc -gctccgagctccgccccgg----------------------------------------- ------------------------------------------------------------- ---------------------------------ccccgccccggcccctgcccgctccgag -ctccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccc -ccgccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgct -ccgagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccg -ccccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcag -ccgctc ->syndip_2_chr20:63641737-63642125 -gctgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgc -ctcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcc -cagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccg -agctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cc -cccgcccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgccc -gctccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttg -ccctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggccca -gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag -ctccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccc -cctccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgct -ccgagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccg -ccccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcag -ccgctc ->p:HG002_1_chr20:63641737-63642125 -gctgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgc -ctcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcc -cagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccg -agctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cc -cccgcccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgccc -gctccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttg -ccctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggccca -gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag -ctccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccc -cctccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgct -ccgagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccg -ccccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcag -ccgctc ->p:HG002_2_chr20:63641737-63642125 -gctgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgc -ctcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcc -cagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccg -agctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cc -cccgcccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgccc -gctccgagctccgccccgg----------------------------------------- ------------------------------------------------------------- ---------------------------------ccccgccccggcccctgcccgctccgag -ctccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccc -ccgccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgct -ccgagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccg -ccccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcag -ccgctc ->ref_chr20:63641737-63642125 -gctgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgc -ctcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgcc -cagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccg -agctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cc -cccgcccagtgccccgccccctgactgctgctagccctgcccccgccccggcccctgccc -gctccgagcttcgccccgg----------------------------------------- ------------------------------------------------------------- ---------------------------------ccccgccccggcccctgcccgctccgag -ctccgccccggccccgcccccgcaccttctcgcgcagcc--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---gctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_69e7c4dc7f053eda2403927861e33459.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_69e7c4dc7f053eda2403927861e33459.msa deleted file mode 100644 index 56caa352..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_69e7c4dc7f053eda2403927861e33459.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:63048933-63049512 -gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca -ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat -gtgggggcagactcctcctcctcctcctcttcctcctcc--------------------- -------tcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcc -tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttccttctcc -tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct -tcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcc -tcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttcctcttcctcc -tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcttcctcc -tcc---------------------------------------tcttcctctttctcctcc -tcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcc -tcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctct -tcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttcctcctcctcc -tcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcc -tcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcc -tcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct-cctcctcttcctc -ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct -tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct -cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag -gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac -tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcagg ->syndip_2_chr20:63048933-63049512 -gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca -ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat -gtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct -tcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcc -tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttcctcctcc -tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct -ttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcc -tcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttcctcttcctcc -tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcctcttcc -tcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctct -tcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcctcctcctcc -tcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcc -tcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttcc -tcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttcc -tcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcc -tcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcct-cctcctcttcctc -ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct -tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct -cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag -gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac -tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcagg ->p:HG002_1_chr20:63048933-63049512 -gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca -ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat -gtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct -tcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcc -tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttcctcctcc -tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct -ttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctcc -tcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttcctcttcctcc -tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcctcttcc -tcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctct -tcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcctcctcctcc -tcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcc -tcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttcc -tcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttcc -tcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcc -tcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcct-cctcctcttcctc -ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct -tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct -cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag -gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac -tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcagg ->p:HG002_2_chr20:63048933-63049512 -gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca -ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat -gtgggggcagactcctcctcctcctcctcttcctcctcc--------------------- -------tcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcc -tcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttccttctcc -tcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctct -tcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcc -tcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttcctcttcctcc -tcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcttcctcc -tcc---------------------------------------tcttcctctttctcctcc -tcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcc -tcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctct -tcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttcctcctcctcc -tcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcc -tcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcc -tcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct-cctcctcttcctc -ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct -tcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcct -cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag -gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac -tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcagg ->ref_chr20:63048933-63049512 -gcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcca -ggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtcat -gtgggggcaga------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------ctcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctct -tcctcttcctcctcctcctcctcttcctcctcctcctcctcttcctccctcctcttcctc -ctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctct -tcctcctcctcctcttcctctcctcctcctcctcctcttcctcctcctcctcctcttcct -cccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttccag -gacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgaccac -tggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggca -ggacccagaagcctggtagaaagtgaccatgtgtggcagg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6b46f8a89c12958c69731d153b2ed254.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6b46f8a89c12958c69731d153b2ed254.msa deleted file mode 100644 index 8c7c1bfa..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6b46f8a89c12958c69731d153b2ed254.msa +++ /dev/null @@ -1,345 +0,0 @@ ->syndip_1_chr20:64131703-64134056 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtaga -gaccccctcactgtcaactctcatgtcctatagagaccccctcactgtcaactctcatgt -cctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccacc -ctcatgtcctata--------------------------------gagaccccctcactg -tccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat-gagaccc -cctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccactctcat -gtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc -tcatgtcctatgagaccccctcactgtccactctcatgtcctat-gagaccccctcactg -tccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctat -agagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcat -gtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtcca -ccctcatgtcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgaga -ccccctcactgtccaccctcatgt------------------------------------ ------------------------------------------------------------- ------cctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactg -tccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccc -cctcactgtccactctcatgtcctatagagacccctcactgtccaccctcatggcctata -gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgt -gtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctca -ctgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagagac -cccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcct -atagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatggc--------------------- ------------------------------------------------------------- -----------------------------------------------------ctgtagag -accccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctat---------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctataga -gaccccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctatagagacc -ccctcactgtccaccctcgtgtcctatagagaccccctcactctccaccctcatgtccta -tagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctc -atgtcctat-gagaccccctcactgtccaccctcatggcctatagagaccccctcactgt -ccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagacccc -ctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactctccaccctcatggcctatagagaccccctcactgtccaccctcgt -gtcctatagagaccccctcactctccaccctcatggcctatagagaccccctcactgtcc -accctcatggcctatagagaccccctcactgtccactctcatgtcctatgagaccccctc -actgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatgaga -ccccctcactgtccactctcatgtcctat-gagaccccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccct -cgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatgagaccccc -tcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatggcctataga -gaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatagagaccccctcactgtccactctcatggcctgtagagaccccctcac -tgtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatt -tgctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaaggg -ccctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc ->syndip_2_chr20:64131703-64134056 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgg -cctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccacc -ctcatgtcctatagagacccctcactgtccaccctcatggcctatgagaccccctcactg -tccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc -cctcactgtccaccctcatgtcctatagaga-cccctcactgtccaccctcatggcctat -gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccctc -actgtccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagag -accccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctcgtgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc -cctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat -agagaccccctcactgtccaccctcgtgtccta--------------------------- ------------------------------------------------------------- --------------tagagaccccctcactgtccaccctcatggcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgaga -ccccctcactgtccaccctcatgg------------------------------------ ------------------------------------------------------------- ------cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactg -tccaccctcatgtcctat------------------------------------------ ------------------------------------------------------------- -gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgt -gtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcatgtcctata--------------------------------------------- ----------------------gagaccccctcactgtccaccctcatggcctatagagac -cccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcct -atagagaccccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctc -atggcctatagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtc -caccctcgtgtcctatgagaccccctcactgtccaccctcatggcctatagagaccccct -cactgtccaccctcatggcctatgagaccccctcactgtccaccctcatggcctgtagag -accccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccactctcatgtcctatagagacccctcactg -tccaccctcatggcctatagagaccccctcactgtccaccctcatggcctatagagaccc -cctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat -agagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctca -tggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatggcctata--------- ------------------------------------------------------------- --------------------------------gagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccacc -ctcatggcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgtgtccta -tagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgt -ccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtcc -accctcatggcctatagagaccccctcactgtccaccctcatggcctatgagaccccctc -actgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagag -acccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcc -tatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccct -catgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata-------- ------------------------------------------------------------- --------------------------------gagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcgtgtcctatagagaccccctcactgtccacccatatggcctgtagagaccccctcac -tgtccaccctcatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatt -tgctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaaggg -ccctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc ->p:HG002_1_chr20:64131703-64134056 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtaga -gaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgg -cctatgagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccacc -ctcatgtcctatagagacccctcactgtccaccctcatggcctatgagaccccctcactg -tccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc -cctcactgtccaccctcatgtcctatagaga-cccctcactgtccaccctcatggcctat -gagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat-gagaccccctc -actgtccactctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagag -accccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctcgtgtcc -tatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccc -tcatgtcctatgagaccccctcactgtccaccctcatgtcctatagagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccc -cctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat -agagaccccctcactgtccaccctcgtgtccta--------------------------- ------------------------------------------------------------- --------------tagagaccccctcactgtccaccctcatggcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgaga -ccccctcactgtccaccctcatgg------------------------------------ ------------------------------------------------------------- ------cctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactg -tccaccctcatgtcctat------------------------------------------ ------------------------------------------------------------- -gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgt -gtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcatgtcctata--------------------------------------------- ----------------------gagaccccctcactgtccaccctcatggcctatagagac -cccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcct -atagagaccccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctc -atggcctatagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtc -caccctcgtgtcctatgagaccccctcactgtccaccctcatggcctatagagaccccct -cactgtccaccctcatggcctatgagaccccctcactgtccaccctcatggcctgtagag -accccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccacc -ctcatgtcctatgagaccccctcactgtccactctcatgtcctatagagacccctcactg -tccaccctcatggcctatagagaccccctcactgtccaccctcatggcctatagagaccc -cctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat -agagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtccaccctca -tggcctgtagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatggcctata--------- ------------------------------------------------------------- --------------------------------gagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccacc -ctcatggcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcact -gtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagacc -ccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcgtgtccta -tagagaccccctcactgtccaccctcatggcctatagagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgt -ccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -gtcctatagagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtcc -accctcatggcctatagagaccccctcactgtccaccctcatggcctatgagaccccctc -actgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctatagag -acccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcgtgtcc -tatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccct -catgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctata-------- ------------------------------------------------------------- --------------------------------gagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcgtgtcctatagagaccccctcactgtccacccatatggcctgtagagaccccctcac -tgtccaccctcatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatt -tgctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaaggg -ccctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc ->p:HG002_2_chr20:64131703-64134056 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccactctcatggcctgtaga -gaccccctcactgtcaactctcatgtcctatagagaccccctcactgtcaactctcatgt -cctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtccacc -ctcatgtcctata--------------------------------gagaccccctcactg -tccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat-gagaccc -cctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccactctcat -gtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ccctcatgtcctatagagaccccctcactgtccaccctcatggcctgtagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccc -tcatgtcctatgagaccccctcactgtccactctcatgtcctat-gagaccccctcactg -tccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgtgtcctat -agagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccactctcat -gtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctcactgtcca -ccctcatgtcctgtagagaccccctcactgtccaccctcgtgtcctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgaga -ccccctcactgtccaccctcatgt------------------------------------ ------------------------------------------------------------- ------cctatagagaccccctcactgtccaccctcatggcctgtagagaccccctcactg -tccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccc -cctcactgtccactctcatgtcctatagagacccctcactgtccaccctcatggcctata -gagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcgt -gtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtcca -ctctcatgtcctatgagaccccctcactgtccactctcatggcctgtagagaccccctca -ctgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtagagac -cccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcct -atagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatggc--------------------- ------------------------------------------------------------- -----------------------------------------------------ctgtagag -accccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctat---------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctca -tgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccct -cactgtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctataga -gaccccctcactgtccaccctcgtgtcctatgagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcact -gtccaccctcgtgtcctatagagaccccctcactgtcaactctcatgtcctatagagacc -ccctcactgtccaccctcgtgtcctatagagaccccctcactctccaccctcatgtccta -tagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctc -atgtcctat-gagaccccctcactgtccaccctcatggcctatagagaccccctcactgt -ccaccctcatgtcctat-gagaccccctcactgtccaccctcatgtcctatagagacccc -ctcactgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctata -gagaccccctcactctccaccctcatggcctatagagaccccctcactgtccaccctcgt -gtcctatagagaccccctcactctccaccctcatggcctatagagaccccctcactgtcc -accctcatggcctatagagaccccctcactgtccactctcatgtcctatgagaccccctc -actgtccaccctcatggcctatagagaccccctcactgtccaccctcatgtcctatgaga -ccccctcactgtccactctcatgtcctat-gagaccccctcactgtccaccctcatggcc -tgtagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccct -cgtgtcctatagagaccccctcactgtccaccctcatgtcctatgagaccccctcactgt -ccaccctcatgtcctatagagaccccctcactgtccactctcatgtcctatgagaccccc -tcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatggcctataga -gaccccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcatgtc -ctatagagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccacc -ctcatgtcctatagagaccccctcactgtccactctcatggcctgtagagaccccctcac -tgtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatt -tgctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaaggg -ccctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc ->ref_chr20:64131703-64134056 -caggctgttgtaggtgggccaggaggggctgggcagcccatgagggtgaggctgagactc -cacactgagcccaggtttaggggacctggtgggggtcacagcctcccctgtcccagactt -ctcctggcctctctcatgtcctatgagaccccctcactgtccaccctcatgtcctgtaga -gaccccctcactgtccactctcatggcctatagagaccccctcactgtccaccctcatgg -cctgta------------------------------------------------------ ----------------------------------------------gagaccccctcactg -tccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatagagaccc -cctcactgtccaccctcatggcctgtagagaccccctcactgtccaccctcatgtcctat -gagaccccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcat -gtcctata---------------------------------------------------- --------------------------------------------------gagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctgtagag -accccctcactgtccaccctcatgtcctatgagaccccctcactgtccaccctcgtgt-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------cctatagagaccccctc -actgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcctatgaga -ccccctcactgtccaccctcatgtcctatagagaccccctcactgtccactctcatgtcc -tatagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtccactct -catggcctatagagaccccctcactgtccaccctcatggcctatagagaccccctcactg -tccaccctcatggcctgt------------------------------------------ ------------------------------------------------------------a -gagaccccctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatggcctatgagaccccctcactgtcca -ccctcatgtcctat---------------------------------------------- ----------------------gagaccccctcactgtccaccctcatgtcctatagagac -cccctcactgtccaccctcgtgtcctatagagaccccctcactgtccaccctcatgtcct -atagagaccccctcactgtccgccctcatgtcctatgagaccccctcactgtccaccctc -atgtcctatagagaccccctcactgtccaccctcatggc--------------------- ------------------------------------------------------------- -----------------------------------------------------ctgtagag -accccctcactgtccgccctcatgtcctat------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------gagaccccctcactgtccaccctcatgtcctgtagagaccccctcactgtc -caccctcatgtcctatagagaccccctcactgtccaccctcatgtcctat---------- ------------------------------------------------------------- --------------------------------gagaccccctcactgtccaccctcatgtc -ctat-gagaccccctcactgtccaccctcatgtcctatgaga------------------ -------------------cccctcactgtccaccctcatgtcctatgagaccccctcact -gtccaccctcatgtcctat----------------------------------------- ------------------------------------------------------------- -------------------------------------gagaccccctcactgtccactctc -atgtcctat-gaga-cccctcactgtccaccctcatgtcctatagagaccccctcactgt -ccaccctcatggcctgtagagaccccctcactgtcaactctcatgtcctat-gagacccc -ctcactgtccaccctcatgtcctatagagaccccctcactgtccaccctcatgtcc---- --------------------------------aaagagaccccctcactgtccaccctcat -ggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtcc -accctcatggcctatagagaccccctcactgtccaccctcatgtccaaagagaccccctc -actgtccaccctcatggcctgtagagaccccctcactgtccaccctcatggcctgta--- -------------------------------gagaccccctcactgtccaccctcatgtcc -tatagagaccccctcactgtccaccctcatgtccaaagagaccccctcactgtccaccct -catggcctgta---------------------------------gagaccccctcactgt -ccacccatatggcctgtagagaccccctcactgtccaccctcatgtcctata-------- ------------------------------------------------------------- --------------------------------gagaccccctcactgtccaccctcatggc -ctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcactgtccacc -ctcatggcctgtagagaccccctcactgtccaccctcatggcctgtagagaccccctcac -tgtccacccatatggcctgtagagaccccctcactgtccaccctcaggaccctctgcatt -tgctccttgggttcccggaacttgagcttgggtcttggtccacagcagctttgggaaggg -ccctcggctgctttttgcttcagcagctggggagcagttaactttcagacccggccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6c04ed8d325a63a5d479c2b59cd68b98.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6c04ed8d325a63a5d479c2b59cd68b98.msa deleted file mode 100644 index f76cdb00..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6c04ed8d325a63a5d479c2b59cd68b98.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:4032247-4033338 -gcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacc -catcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagt-------- ---------------------------------gaggagcgtctctgcccggccgccatcc -catctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcg -tctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtc -tgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctc -tgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctga -gaagtgaggagcccctccgtccggcaaccaccccgt------------------------ ------------------------------------------------------------- ----ctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggtgggg -ggggtcagccccccgcccggccagccgccccgtccgggaggtgaggggctcctctgcccg -gccgcccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggaggg -aggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcccc -ccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctact -gggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggtc -agccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcc -cctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgg -gggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagcc -ccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccggc -cagccgccccgtccgggagggaggt-gggggggggtcagccccccgcccggcca-gccgc -cccgtccgggagggaggtggggggatcagccccccgcctggccagccgccccgtccggga -ggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctctgcccggc -cagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccgggag -ggaggtgggggggtcagccccctttccggcc--gccgcctgtccgggaggtgaggggcgc -ctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtc -cgggagggaggtgggggggacagcccc ->syndip_2_chr20:4032247-4033338 -gcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacc -catcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcg -tctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcc -catctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcg -tctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtc -tgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctc -tgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctga -gaagtgaggagcccctccgtccggcaaccaccccgt------------------------ ------------------------------------------------------------- ----ctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt---- ------------------------------------------------------------- ------------------------------------------------------------- -----gggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcccc -ccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctact -gggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggtc -agccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcc -cctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgg -gggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagcc -ccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccggc -cagccgccccgtccgggagggaggtgggggggggggtcagccccccgcccggccagccgc -cccgtccgggagggaggtggggggatcagccccccgcctggccagccgccccgtccggga -ggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctctgcccggc -cagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccgggag -ggaggtgggggggtcagccccctttccggcc--gccgcctgtccgggaggtgaggggcgc -ctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtc -cgggagggaggtgggggggacagcccc ->p:HG002_1_chr20:4032247-4033338 -gcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacc -catcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcg -tctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcc -catctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcg -tctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtc -tgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctc -tgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctga -gaagtgaggagcccctccgtccggcaaccaccccgt------------------------ ------------------------------------------------------------- ----ctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt---- ------------------------------------------------------------- ------------------------------------------------------------- -----gggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcccc -ccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctact -gggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggtc -agccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcc -cctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgg -gggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagcc -ccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccggc -cagccgccccgtccgggagggaggtggggggggggtcagccccctttccggcccagccgc -cccgtccgggagggaggtggggggatcagccccccgcctggccagccgccccgtccggga -ggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctctgcccggc -cagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccgggag -ggaggtgggggggtcagccccccttccggccgggccgcctgtccgggaggtgaggggcgc -ctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtc -cgggagggaggtgggggggacagcccc ->p:HG002_2_chr20:4032247-4033338 -gcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacc -catcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcg -tctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcc -catctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcg -tctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtc -tgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctc -tgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctga -gaagtgaggagcccctccgtccggcaaccaccccgtccgggagggaggtggggggggtca -gccccccgcccggccagccgccccgtccgggaggtgaggggctcctctgcccggccgccc -ctactgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt---- ------------------------------------------------------------- ------------------------------------------------------------- -----gggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcccc -ccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctact -gggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggtc -agccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcc -cctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgg -gggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagcc -ccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccggc -cagccgccccgtccgggagggaggt-ggggggggggtcagccccctttccggcc-gccgc -cccgtccgggagggaggtggggggatcagccccccgcctggccagccgccccgtccggga -ggtgaggggcgcctctgcccggccacccctactgggaagtgaggagcccctctgcccggc -cagccgccccgtccgggagggaggcgggggggggggtcggccagccgccccgtccgggag -ggaggtgggggggtcagccccccttccggccggccgccctgtccgggaggtgaggggcgc -ctctgcctggccgcccctactgggaagtgaggacccctctgcccggccagccgccccgtc -cgggagggaggtgggggggacagcccc ->ref_chr20:4032247-4033338 -gcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctctgcttggccacc -catcgtctgggatatgaggagcccctctgcctggctgcccagtctggaaagtgaggagcg -tctctgcccggccgccatcccatctaggaagcgaggagcgtctctgcccggccgccatcc -catctaggaagcgaggagcgcctcttcccggctgccatcccatctaggaactgaggagcg -tctctgcccggccgcccatcgtctgagatgtggggagcacctctgccccaccgccctgtc -tgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtgaggagcgtctc -tgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaaccgccccgtctga -gaagtgaggagcccctccgtccggcaaccaccccgt------------------------ ------------------------------------------------------------- ----ctgggaagtgaggagcgtctccgcccggcagccaccccgtccgggagggaggt---- ------------------------------------------------------------- ------------------------------------------------------------- -----gggggggggggtcggccagccgccccgtccgggagggaggtgggggggtcagcccc -ccgcccggccggccgccccgtccgggaggtgaggggcgcctctgcccggccgcccctact -gggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggggggtc -agccccccgcccggccggctgccccgtccgggaggtgaggggcgcctctgcccggccgcc -cctactgggaagtgaggagcccctctgcccggccagctgccccgcccgggagggaggtgg -gggggtcagccccccgcctggccagccgccccatccgggagggaggtgggggggtcagcc -ccccgcccggccagccgccccgtccgggaggggggagggggggtcagccccctgcccggc -cagccgccccgtccgggagggaggt-ggggggggggtcagccccctttccggcc-gccg- --------------------------------------------------cctgtccggga -ggtgaggggcgcctctgcctggccgcccctactgggaagtgagga-cccctctgcccggc -cagccgccccgtccgggagggaggtgggggggacagcc---------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------cc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6d15d31a96c87ab736365079455231cc.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6d15d31a96c87ab736365079455231cc.msa deleted file mode 100644 index d1ab926d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6d15d31a96c87ab736365079455231cc.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:53203989-53204362 -cgtagtgcacaatatctccttcatttttataatatgatactattatatcataattttata -atatactattatatcatattatatgatactatttatatcatcatatgatgatatactat- --tatatcatcatatgatgatata--ctattatatcatcatatgatgatatg--atactat -atcatcatatgatgatatgatactatatcatcatatgatgat---atactatatcatcat -atgatgatatgatatactatatcatcatatgatgatatgatactatatcatcat-----a -tgatgatatgatactatatcatcat-----atgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcacatgatgatatgatactat -atcatcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcac -atgatgatatgatactatatcatcacatgatgatatgatactatatcatcacatgatgat -atgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatact -atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata -ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga -tacta------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------- ->syndip_2_chr20:53203989-53204362 -cgtagtgcacaatatctccttcatttttataatatgatactattatatcataattttata -atatactattatatcatattatatgatactatttatatcatcatatgatgatatgatat- --tatatcatcatatgatgatatg--atactatatcatcatatgatgatatgatatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatg--atactatatcatcatatgatgatatgatactatatcatcat-----a -tgatgatatgatactatatcatcat-----atgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcat-----atgatgatatgatactatatcatcat-----atgatgatatgata -ctatatcatcat-----atgatgatatgatactatatcatcatatgatgatatgatacta -tatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcataa -catgatgatatgatactatatcataacatgatgatatgatactatatcatcatataacat -gatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatataac -atgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatata -acatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatacta ->p:HG002_1_chr20:53203989-53204362 -cgtagtgcacaatatctccttcatttttataatatgatactattatatcataattttata -atatactattatatcatattatatgatactatttatatcatcatatgatgatatgatata -ctatatcatcatatgatgatatgatatactatatcatcatatgatgatatg--atactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatg--atactatatcatcatatgatgatatgatactatatcatcat-----a -tgatgatatgatactatatcatcat-----atgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcat-----atgatgatatgatactatatcatcat-----atgatgatatgata -ctatatcatcat-----atgatgatatgatactatatcatcatatgatgatatgatacta -tatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcataa -catgatgatatgatactatatcataacatgatgatatgatactatatcatcatataacat -gatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatataac -atgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatata -acatgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcata -taacatgatgatatgatactatatcatcatataacatgatgatatgatacta ->p:HG002_2_chr20:53203989-53204362 -cgtagtgcacaatatctccttcatttttataatatgatactattatatcataattttata -atatactattatatcatattatatgatactatttatatcatcatatgatgatatgatata -ctatatcatcatatgatgatatg----attatatcatcatatgatgatatg--atactat -atcatcatatgatgatatgatactatatcatcatatgatgat---atactatatcatcat -atgatgatatg--atactatatcatcatatgatgatatgatactatatcatcat-----a -tgatgatatgatactatatcatcat-----atgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatat -gatactatatcatcatatgatgatatgatactatatcatcacatgatgatatgatactat -atcatcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcac -atgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata -ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga -tacta------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------- ->ref_chr20:53203989-53204362 -cgtagtgcacaatatctccttcatttttataatatgatactattatatcataattttata -atatactattatatcatattatatgatactatttatatcatcatatgatgatatgatata -ctatatcatcatatgatgatatgatatactatatcatcatatgatgatatg--atactat -atcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcat -atgatgatatg--atactatatcatcatatgatgatatgatactatatcatcatataaca -tgatgatatgatactatatcatcatataacatgatgatatgatactatatcatcatataa -catgatgatatgatacta------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6d1c1308371f4f9caaeefc921fbafc4f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6d1c1308371f4f9caaeefc921fbafc4f.msa deleted file mode 100644 index 5698dac8..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6d1c1308371f4f9caaeefc921fbafc4f.msa +++ /dev/null @@ -1,205 +0,0 @@ ->syndip_1_chr20:63948413-63948859 -cacagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagc -aagctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccg -ccatgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggg -a-ggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggaggg -gcgtgtgtgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtgaggggcgt -gtgtgagagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgt -gagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgaga -ggg-----------------aggggcgtgtgtgtgagggaggggcgtgtgagag-ggagg -gggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtg -tgtgagagggagggggcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt-- ---gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgag -acggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagag -ggaggggcgtgtgtgagggagggg---gcgtgtgagagggaggggcgtgtgtgagaggga -gggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgtgtgagagggaggggcgtgtgagaggg-aggggcgtgtgtgagagg--------- --gagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaaggg -aggggcgtgtgtgagagggagggggcgtgagagggaggggcgtgtgtgagagggaggggc -gtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgt -gtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtg -agag--------ggagggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgt -gtgtgagaggga-ggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgt -gagagggagggggcgtgtgtgagagggagggggcgtgt-------------gtgagaggg -agaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggagag -gcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggc -gtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg -tgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgt -gagagggaggggcgtgtgtgagagggag--------------ggggcgtgtgtgagaggg -aggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga- -ggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggc -gtgtgtgagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgag -agggagggggcgtg-----agagggaggggcgtgtgtgagagggaggggcgtgtgtgaga -gggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagg -gaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggaggg -g-gcgtgtgagagggaggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcg -tgtgtgagaggga-ggggcgtgtgtgagagggagggg-cgtgtgtgagagggaggggcgt -gagagggagggggcgtgtgt--gagggaggggcgtgtgtgagaggga-ggggggcgtgtg -tgagagggagggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgta -agggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcact -ctctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcagg -tgccactttgttgccataaaccaaaccgtagtctgt ->syndip_2_chr20:63948413-63948859 -cacagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagc -aagctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccg -ccatgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggg -agggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggaggg -gcgtgtgtgagagggagggggcgtgtgtgaaagggaggggcgtgtgtgagggaggggcgt -gtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgt -gagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgagg -gggggcgtgtgtgagagggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggag -gggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtg -tgtgag-gggggggcgtgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtga -gagggagggggcgtgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga- ---agggaggggtgtgtgtgagagtgggggcgtgtgtgagaggg--------gcgtgagag -gtaggggcgtgtgtgagagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga --ggggcgtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgtgtgagagggaggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtg -agggggggcgtgtgtgagaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-aggg -aggggcgtgtgtgagaggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggc -gtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgt -gtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag -gggggcgtgtgagagggaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgt -gtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgt -gtgaagggaggggtgtgtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggt -aggggcgtgtgtgagagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggaggg -gcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggc -gtgtgtgagggagggggcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtg -tgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgt -gagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtga---gg -gggggcgtgtgtgagaggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggag -ggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt-------------- ------------------gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgag -agggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-a -gggaggggcgtgtgtgagagtgggggcgtgtgtgagaggg----------gcgtgagagg -taggggcgtgtgtgagagggagggg-gcgtgagagggaggggcgtgtgtgagagggaggg -gcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcg -tgtgtgagagggagggggcgtgtgtgagagggagggg-cgtgt---------------gt -gagagggaaggggcgtgtga--gagggaggggcgtgtgtgagaggga-ggggcgtgtgtg -aga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgta -agggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcact -ctctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcagg -tgccactttgttgccataaaccaaaccgtagtctgt ->p:HG002_1_chr20:63948413-63948859 -cacagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagc -aagctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccg -ccatgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggg -agggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggaggg -gcgtgtgtgagagggagggggcgtgtgtgaaagggaggggcgtgtgtgagggaggggcgt -gtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgt -gagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgagg -gggggcgtgtgtgagagggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggag -gggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtg -tgtgag-gggggggcgtgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtga -gagggagggggcgtgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga- ---agggaggggtgtgtgtgagagtgggggcgtgtgtgagaggg--------gcgtgagag -gtaggggcgtgtgtgagagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga --ggggcgtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgtgtgagagggaggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtg -agggggggcgtgtgtgagaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-aggg -aggggcgtgtgtgagaggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggc -gtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgt -gtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag -gggggcgtgtgagagggaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgt -gtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgt -gtgaagggaggggtgtgtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggt -aggggcgtgtgtgagagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggaggg -gcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggc -gtgtgtgagggagggggcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtg -tgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgt -gagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtga---gg -gggggcgtgtgtgagaggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggag -ggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt-------------- ------------------gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgag -agggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-a -gggaggggcgtgtgtgagagtgggggcgtgtgtgagaggg----------gcgtgagagg -taggggcgtgtgtgagagggagggg-gcgtgagagggaggggcgtgtgtgagagggaggg -gcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcg -tgtgtgagagggagggggcgtgtgtgagagggagggg-cgtgt---------------gt -gagagggaaggggcgtgtga--gagggaggggcgtgtgtgagaggga-ggggcgtgtgtg -aga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgta -agggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcact -ctctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcagg -tgccactttgttgccataaaccaaaccgtagtctgt ->p:HG002_2_chr20:63948413-63948859 -cacagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagc -aagctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccg -ccatgcgcctcggtgtgaggagggaggcgtgtgtgagagggaggggcgtgtgtgagaggg -a-ggggcgtgtgtgagagggaggggcgtgtgtgagggaggggtgtgtgtgagagggaggg -gcgtgtgtgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtgaggggcgt -gtgtgagagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgt -gagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgaga -ggg-----------------aggggcgtgtgtgtgagggaggggcgtgtgagag-ggagg -gggcgtgtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtg -tgtgagagggagggggcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt-- ---gggagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgag -acggaggggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagag -ggaggggcgtgtgtgagggagggg---gcgtgtgagagggaggggcgtgtgtgagaggga -gggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggg -gcgtgtgtgagagggaggggcgtgtgagaggg-aggggcgtgtgtgagagg--------- --gagggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaaggg -aggggcgtgtgtgagagggagggggcgtgagagggaggggcgtgtgtgagagggaggggc -gtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgt -gtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtg -agag--------ggagggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgt -gtgtgagaggga-ggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgt -gagagggagggggcgtgtgtgagagggagggggcgtgt-------------gtgagaggg -agaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggagag -gcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggc -gtgtgtgagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtg -tgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgt -gagagggaggggcgtgtgtgagagggag--------------ggggcgtgtgtgagaggg -aggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga- -ggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggc -gtgtgtgagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgag -agggagggggcgtg-----agagggaggggcgtgtgtgagagggaggggcgtgtgtgaga -gggaggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagg -gaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggaggg -g-gcgtgtgagagggaggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcg -tgtgtgagaggga-ggggcgtgtgtgagagggagggg-cgtgtgtgagagggaggggcgt -gagagggagggggcgtgtgt--gagggaggggcgtgtgtgagaggga-ggggggcgtgtg -tgagagggagggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgta -agggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcact -ctctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcagg -tgccactttgttgccataaaccaaaccgtagtctgt ->ref_chr20:63948413-63948859 -cacagaacacaggtgcggacagggaacggcatcctcagagcatggtcaggggagaaaagc -aagctggaaggagagatgattccatctgtataaaatccaggaaacgaaggacgctcaccg -ccatgcgcctcg------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- 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------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----gtgtgaggagggaggcgtgtgtgagagggaggggatgtgt---------------gt -gagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaaggggcgtgtgtg -aga---gggaggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgta -agggagggggtgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcact -ctctggccaccaagatttggaacagcaacttctgtcacatttgaatgtttttaaagcagg -tgccactttgttgccataaaccaaaccgtagtctgt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6e8e602a26dd60ed6f043a31dd9b5ce9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6e8e602a26dd60ed6f043a31dd9b5ce9.msa deleted file mode 100644 index a0ceb6fc..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6e8e602a26dd60ed6f043a31dd9b5ce9.msa +++ /dev/null @@ -1,145 +0,0 @@ ->syndip_1_chr20:61282405-61283770 -cataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaac -agaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccactttta -atctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgt -acttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtattgtgttc -atatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgc -atgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtat -gcacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcac -gtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgt -gcatttgcacgcatgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgt -gtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgttt -gcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgt------------- -------------------------gtgctgtggcgtgtgtgatgtacgtgcgtttgcacg -cgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg---------- -------gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgt -gcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggc -gtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgttt -gcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtg -tgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgca -cgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgt -gatgtgtgtgcgtttgcacgcgtgtgc--------------------------------- ---------------------------------------------------tgtgtgatgt -gtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgct -gtggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcg -tttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgct -ctcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcat -catttctttgtgatgggtcattagaagcaggattctgaatt ->syndip_2_chr20:61282405-61283770 -cataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaac -agaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccactttta -atctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgt -acttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttc -atatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgc -atgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtat -gcacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcac -gtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgt -gcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgt -gtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgttt -gcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtg -tgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacg -cgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtga -tgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggc -gtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgttt -gcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtg -tgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgca -cgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgt -gatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgc -gtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgt -aggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgct -gtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgca -tttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgct -ctcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcat -catttctttgtgatgggtcattagaagcaggattctgaatt ->p:HG002_1_chr20:61282405-61283770 -cataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaac -agaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccactttta -atctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgt -acttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttc -atatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgtttagatgtgc -atgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtat -gcacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcac -gtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgt -gcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgt -gtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgttt -gcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtg -tgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacg -cgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtga -tgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggc -gtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgttt -gcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtg -tgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgca -cgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgt -gatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgc -gtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgt -aggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgct -gtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgca -tttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgct -ctcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcat -catttctttgtgatgggtcattagaagcaggattctgaatt ->p:HG002_2_chr20:61282405-61283770 -cataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaac -agaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccactttta -atctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgt -acttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtattgtgttc -atatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcggatgtgc -atgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtat -gcacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcac -gtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgt -gcatttgcacgcatgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgt -gtgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgttt -gcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgt------------- -------------------------gtgctgtggcgtgtgtgatgtacgtgcgtttgcacg -cgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg---------- -------gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgt -gcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggc -gtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgttt -gcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtg -tgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgca -cgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgt -gatgtgtgtgcgtttgcacgcgtgtgc--------------------------------- ---------------------------------------------------tgtgtgatgt -gtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgct -gtggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcg -tttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgct -ctcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcat -catttctttgtgatgggtcattagaagcaggattctgaatt ->ref_chr20:61282405-61283770 -cataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaac -agaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccactttta -atctttggcatggtgtgtgtgcatgtgtgtgtgtgtgtgtgtgtgtgtatgtctatctgt -acttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttc -atatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgc -atgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtat -gcacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcac -gtgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgt -gcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgt -g----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------gcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg---------- -------gcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgt -gcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgt -ggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcg -tttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc -gtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgttt -gcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc--- -------gtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgca -cgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgt -gatgtgtgtgcgtttgcacgcgtgtgc--------------------------------- ----------------------------------------------tgtggtgtgtgatgt -aggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgct -gtggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgca -tttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgct -ctcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcat -catttctttgtgatgggtcattagaagcaggattctgaatt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_6fecb38e42c1fb0e27f26e0c7db37b3a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_6fecb38e42c1fb0e27f26e0c7db37b3a.msa deleted file mode 100644 index 12b6b8ba..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_6fecb38e42c1fb0e27f26e0c7db37b3a.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:10802576-10803058 -gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt -tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca -atgtcctctgaatatatatatatatatcctccc----------atatatatatatatcct -ccc--atatatatatatatat--------------------------------------- ------------------------------atatatatatatatgtcctcccatatatata -tatatcctcccatatatatatctatcctccc----atatatatatatatatattttcaat -gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac -ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caa ->syndip_2_chr20:10802576-10803058 -gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt -tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca -atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct -ccc--atatatatatatatatatatatatcctcccatatatatatatatatatatatcct -cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata -tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat -gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac -ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caa ->p:HG002_1_chr20:10802576-10803058 -gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt -tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca -atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct -ccc--atatatatatatatatatatatatcctcccatatatatatatatatatatatcct -cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata -tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat -gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac -ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caa ->p:HG002_2_chr20:10802576-10803058 -gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt -tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca -atgtcctctgaatatatatatatatatcctccc----------atatatatatatatcct -ccc--atatatatatatatat--------------------------------------- ------------------------------atatatatatatatgtcctcccatatatata -tatatcctcccatatatatatctatcctccc----atatatatatatatatattttcaat -gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac -ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caa ->ref_chr20:10802576-10803058 -gcccaacttaatccagtgtgactccattttaaatcaattatatctgcaaagatctaattt -tcaaatgaggtcacagtcacaagtattgggggttaggacttttgggggacataacccaca -atgtcctctgaatatatatatatatatcctcccatatatatatatatatatatatatcct -cccatatatatatatatatatatatatatcctcccatatatatatatatatatatatcct -cccatatatatatatatatatgtcctcccatatatatatatatatcctcccatatatata -tatatcctcccatatatatatctatcctcccatatatatatatatatatatattttcaat -gtatccctttattcaagtgattttaagcaatgaaagcaagacagctgttataggatttac -ctttctagatggaaaaggacaagtaaataaggtcttaagctccatgtcaagaaaggggca -caa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7056837508170f4bd90cfdaf011cdfc7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7056837508170f4bd90cfdaf011cdfc7.msa deleted file mode 100644 index 379a32fd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7056837508170f4bd90cfdaf011cdfc7.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:55624698-55625762 -tagtataactattataatatttatagtatattatactatataatacagtatactgtatta -tatactataatctactagattataatatactatataatcagtatactatattatatagta -tagtataatatagtattatattatagtaatatattataaagtattatagtaatatagtat -aatatactatacattatatagtatagtatattatatagtatactatatataagtatattt -aatagtatattgtatatagtaattatatatagtatatataatatacaatgtatagtatat -tatagtatactatacgatactgtagtatagtatgctatatagtatactatatacgacagt -atcatatagtatactacaaaatatatagtatagcatagtatactatataatatactatat -tatatatactatattatatatactatactatattatatatactatattatatatactata -ctatacataaaatactatatatagtatattatatatagtatactatatatagtatatata -gtatactatatatactatatatagtatactatatagtatactatatatagtatatatagt -atactatatatagtatactatatatagtatatatatagtatactatatatagtatactat -atatagtatatatagtatactatatatagtatactatatatagtatatatagtatactat -atatagtatactatatatagtatatatagtatactatatatagtatactatatatagtat -atatagtatactatatatagtatatatagtatactatatatagtatatatagtatactat -atatactatatatactata-----------tatagtatactatatatacta--tatatag -tatactatatatcatatatagtattatatacagtatactatatataatatagtatactat -actata-atatactatttgttataattatctagtatagtatactatatatactatattat -atagtatatagtatatatagtatatagtatatatactatatactatatatactatatact -atactatataatatatatactaaataaatataatatacttatttaaatatatttaaataa -atata--aaatatttaaatataattacttaaatatatatttaaaatatttaataaacata -tatttaaatatttatttaatatttaaatattaaatatatataattaatataattatatat -atattatatactatatattatatatact-----atatactatatatagtatactaatata -atatactatatatactatatataatatactatatatagtatatatagtatagtatac--- --tata------atatactatatt--------------------------atataatata- -----------gtatactatatattgtatactatactatgctatagtatgctatatactac -actatagtatactg-----tatactatagtatacagtatactatatactatactatagta --------------tatagtatactatatactatagtatagtatatagtatactgtatact -atagtatagtatactatatactatactatactatagtatactctatagtatataaagaca -tatatatagtcttcaaaatgaagatcctgtatcctatatatatatataacttca ->syndip_2_chr20:55624698-55625762 -tagtataactattataatatttatagtatattatactatataatacagtatactgtatta -tatactataatctactagattataatatactatataatcagtatactatattatatagta -tagtataatatagtattatattatagtaatatattataaagtattatagtaatatagtat -aatatactatac-----------------attatatagtatactatatataagtatattt -aatagtatattgtatatagtaattatatatagtatatataatatacaatgtatagtatat -tatagtatactatacgatactgtagtatagtatgctatatagtatactatatacgacagt -atcatatagtatactacaaaatatatagtatagcatagtatactatataatatactatat -tatatatactatattatatatactatac-----tatacataaaatactatatatagtata -ttatatatagtatactatatatagtatatatagtatactatatatcatatatagtattat -ataca------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -gtatactatatataatatagtatactatactataatatactatttgttataattatctag -tatagtatactatatatactatattatatagtatatatagtatatagtata-tatactat -atactatatatactatatactatact-----------atataatatatatactaaat--- ------------------------------------------------------------- -------------------------------aaatatacttatttaaatatatttaaataa -atatattaaatatttaaatataattacttaaatatatatttaaaatatttaataaacata -tatttaaatatttatttaatatttaaatattaaatatatataattaatataattatatat -atattatatactatatattatatatactatataatatactatatatagtatactaatata -atatactatatatactatatataatatactatatatagtatatatagtatagtatac--- --tata------atatactatatatagtatatatagtatagtatactataatatactatat -atagtatatagtatactatatattgtatactatactatgctatagtatgctatatactac -actatagtatactgtgtactatactatagtatacagtatactatatactatactatagta -tagtatactatagtatagtatactatatactatagtatagtatatagtatactgtatac- -----tatagtatactatatactatactatactatagtatactctatagtatataaagaca -tatatatagtcttcaaaatgaagatcctgtatcctatatatatatataacttca ->p:HG002_1_chr20:55624698-55625762 -tagtataactattataatatttatagtatattatactatataatacagtatactgtatta -tatactataatctactagattataatatactatataatcagtatactatattatatagta -tagtataatatagtattatattatagtaatatattataaagtattatagtaatatagtat -aatatactatac-----------------attatatagtatactatatataagtatattt -aatagtatattgtatatagtaattatatatagtatatataatatacaatgtatagtatat -tatagtatactatacgatactgtagtatagtatgctatatagtatactatatacgacagt -atcatatagtatactacaaaatatatagtatagcatagtatactatataatatactatat -tatatatactatattatatatactatactatattatatatactatattatatatactata -ctatacataaaatactatatatagtatattatatatagtatactatatatagtatataat -atata------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -gtatactatatatactata-----------tatagtatactatatatacta--tatatag -tatactatatatcatatatagtattatatacagtatactatatataatatagtatactat -actata-atatactatttgttataattatctagtatagtatactatatatactaaat--- ------------------------------------------------------------- -------------------------------aaatatacttatttaaatatatttaaataa -atatattaaatatttaaatataattacttaaatatatatttaaaatatttaataaacata -tatttaaatatttatttaatatttaaatattaaatatatataattaatataattatatat -atattatatactatatattatatatactatataatatactatatatagtatactaatata -atatactatatatactatatataatatactatatatattatatagtatatagtatatata -gtatatagtatatatactatatactatatatactatatactatact---atataatatat -atacta-----------atatattgtatactatactatgctatagtatgctatatactac -actatagtatactgtgtactatactatagtatacagtatactatatactatactatagta -tagtatactatagtatagtatactatatactatagtatagtatatagtatactgtatac- -----tatagtatactatatactatactatactatagtatactctatagtatataaagaca -tatatatagtcttcaaaatgaagatcctgtatcctatatatatatataacttca ->p:HG002_2_chr20:55624698-55625762 -tagtataactattataatatttatagtatattatactatataatacagtatactgtatta -tatactataatctactagattataatatactatataatcagtatactatattatatagta -tagtataatatagtattatattatagtaatatattataaagtattatagtaatatagtat -aatatactatacattatatagtatagtatattatatagtatactatatataagtatattt -aatagtatattgtatatagtaattatatatagtatatataatatacaatgtatagtatat -tatagtatactatacgatactgtagtatagtatgctatatagtatactatatacgacagt -atcatatagtatactacaaaatatatagtatagcatagtatactatataatatactatat -tatatatactatattatatatactatactatattatatatactatattatatatactata -ctatacataaaatactatatatagtatattatatatagtatactatatatagtatataat -atatactatatatactatatatagtatactatatagtatactatatatagtatatatagt -atactatatatagtatactatatatagtatatatatagtatactatatatagtatactat -atatagtatatatagtatactatatatagtatactatatatagtatatatagtatactat -atatagtatactatatatagtatatatagtatactatatatagtatactatatatagtat -atatagtatactatatatagtatatatagtatactatatatagtatatatagtatactat -gtatactatatatactata-----------tatagtatactatatatacta--tatatag -tatactatatatcatatatagtattatatacagtatactatatataatatagtatactat -actata-atatactatttgttataattatctagtatagtatactatatatactatattat -atagtatatagtatatatagtatatagtatatatactatatactatatatactatatact -atactatataatatatatactaaataaatataatatacttatttaaatatatttaaataa -atata--aaatatttaaatataattacttaaatatatatttaaaatatttaataaacata -tatttaaatatttatttaatatttaaatattaaatatatataattaatataattatatat -atattatatactatatattatatatact-----atatactatatatagtatactaatata -atatactatatatactatatataatatactatatatagtatatatagtatagtatac--- --tata------a------------------------------------------------ ------------tatactatatattgtatactatactatgctatagtatgctatatactac -actatagtatactgtgtactatactatagtatacagtatactatatactatactatagta -tagtatactatagtatagtatactatatactatagtatagtatatagtatactgtatact -atagtatagtatactatatactatactatactatagtatactctatagtatataaagaca -tatatatagtcttcaaaatgaagatcctgtatcctatatatatatataacttca ->ref_chr20:55624698-55625762 -tagtataactattataatatttatagtatattatactatataatacagtatactgtatta -tatactataatctactagattataatatactatataatcagtatactatatt-----gta -tagtataatatagtattatattatagtaatatattataaagtattatagtaatatagtat -aatatactatacattatatagtatagtatattatatagtatactatatataagtatattt -aatagtatattgtatatagtaattatatatagtatatataatatacaatgtatagtatat -tatagtatactatacgatactgtagtatagtatgctatatagtatactatatacgacagt -atcatatagtatactacaaaatatatagtatagcatagtatactatataatatactatat -tatatatactatattatatatactatactatattatatatactatattatatatactata -ctatacataaaatactatatatagtatattatatatagtatactatatatagtatataat -atata------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -gtatactatatatactata-----------tatagtatactatatatacta--tatatag -tatactatatatcatatatagtattatatacagtatactatatataatatagtatactat -actata-atatactatttgttataattatctagtatagtatactatatatactatat--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------tatatagtatatagtatatata -gtatatagtatatatactatatactatatatactatatactatact---atataatatat -atacta-----------atatattgtatactatactatgctatagtatgctatatactac -actatagtatactgtgtactatactatagtatacagtatactatatactatactatagta -tagtatactatagtatagtatactatatactatagtatagtatatagtatactgtatact -atagtatagtatactatatactatactatactatagtatactctatagtatataaagaca -tatatatagtcttcaaaatgaagatcctgtatcctatatatatatataacttca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_712640f59e8f34dcd1e53c5c9cde985f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_712640f59e8f34dcd1e53c5c9cde985f.msa deleted file mode 100644 index b7082a4f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_712640f59e8f34dcd1e53c5c9cde985f.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:34235649-34236314 -tagcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccc -aggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacag -agtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaa -gaaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaa -ggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaa -tgaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagg -aaggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaa -gaaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaa -aggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaa -aaggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaa -aagaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctcta -ggtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataa -tcccagcactttgggaggccgaagcgggc ->syndip_2_chr20:34235649-34236314 -tagcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccc -aggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacag -agtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaa -gaaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaa -ggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaa -tgaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagg -aaggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaa -gaaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaa -aggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaa -aaggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaa -aagaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctcta -ggtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataa -tcccagcactttgggaggccgaagcgggc ->p:HG002_1_chr20:34235649-34236314 -tagcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccc -aggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacag -agtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaa -gaaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaa -ggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaa -tgaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagg -aaggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaa -gaaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaa -aggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaa -aaggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaa -aagaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctcta -ggtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataa -tcccagcactttgggaggccgaagcaggc ->p:HG002_2_chr20:34235649-34236314 -tagcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccc -aggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacag -agtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaa -gaaagaaagaaggaaggaaggaaggaaggaaggaaggaaggaaggaaggaagggaaggaa -ggaaggaaggaaggaagcgggagggagggaagaaggaaggaaggaggagggagggaagaa -tgaaggaaggaaggaaggagggaaggaaggaaggaagcgggagggagggaagaaggaagg -aaggaaggaaggagggagggagggaagaaggaaggaggagggagggagggaagcaggaaa -gaaggaaggaaggagaaagagagaa--agagagagaagaagaaagagaaagaaacagaaa -aggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggagaaagaaaggaa -aaggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaa -aagaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctcta -ggtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataa -tcccagcactttgggaggccgaagcaggc ->ref_chr20:34235649-34236314 -tagcgcatgcctgtggcccctactactcaggaggcaggggtgggaggattgctagagccc -aggaagtcgtggctgaagtgggctcatgataatgccactgcactccagcctgtgtgacag -agtgagactctgagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaa -gaaagaaagaaagaaggaaggaaggaaggaaggaaggaaaggaaggaaggaaggaaggaa -ggaaggaagga------------------------------------------------- -------aaggaaggaaggaaggaaggaaggaaggaagcgggagggagggaagaaggaagg -aaggaaggaaggagggagggagggaaga--------------------------aggaaa -gaaggaaggaaggagaaagagagaaagagagagagaagaagaaagagaaagaaacagaaa -aggaaggaaggagagagagaaagaaagagaaagagaaggaaggaaggaaggagaaag--a -aaggaaaggaaaggagtggaaaggaaaggagaggaaaggagaaaggagggagggagggaa -aagaaagaaagaaagaaaaggctaaacctgactatgatattgaatttactgctagctcta -ggtggtttaaatgattcaagaatcatggccatggctgggcgcagtggctcacgcctataa -tcccagcactttgggaggccgaagcgggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_71d3a3cbc7c7089cca081c650f00a2a6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_71d3a3cbc7c7089cca081c650f00a2a6.msa deleted file mode 100644 index ac4698d9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_71d3a3cbc7c7089cca081c650f00a2a6.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:50775444-50776123 -tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa -aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc -caaagatttcc--------------------atatatatatatatatatatataaatata -aatatattctatatattcatatatatatattctatatattcatatatataaatatattct -atatattcatatatataaatatattctatatattcatatataaatatattccatatatat -aaatatattccatatatttatatataaatatatatcatatatttatatataaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta -tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat -atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat -taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt -tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt -gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -t ->syndip_2_chr20:50775444-50776123 -tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa -aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc -caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata -aatatattctatatattcatatatatatattctatatattcatatatataaatatattct -atatattcatatatataaatatattctatatattcatatataaatatattccatatatat -aaatatattc-------------------------catatatttatatataaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta -tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat -atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat -taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt -tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt -gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -t ->p:HG002_1_chr20:50775444-50776123 -tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa -aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc -caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata -aatatattctatatattcatatatatatattctatatattcatatatataaatatattct -atatattcatatatataaatatattctatatattcatatataaatatattccatatatat -aaatatattc-------------------------catatatttatatataaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta -tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat -atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat -taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt -tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt -gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -t ->p:HG002_2_chr20:50775444-50776123 -tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa -aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc -caaagatttcc--------------------atatatatatatatatatatataaatata -aatatattctatatattcatatatatatattctatatattcatatatataaatatattct -atatattcatatatataaatatattctatatattcatatataaatatattccatatatat -aaatatattccatatatttatatataaatatatatcatatatttatatataaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta -tatataaatatatatcatatatttatatataaatatatatcatatatttatatataatat -atatcatatattatatataaatatatatcatatatttatatataaatatatatcatatat -taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt -tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt -gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -t ->ref_chr20:50775444-50776123 -tgaacaaagtgaactaatagtagttcacgaaatctactggtttataatgtcacataccaa -aggcttgtgtctttaaatctatctctagacttggtattctgctttctcattctgtctctc -caaagatttccatatatatatatatatatatatatatatatatatatatatataaatata -aatatattctatatattcatatat---------------------------atatattct -atatattcatatatataaatatattctatatattcatatataaatatattccatatatat -aaatatattc-------------------------catatatttatatataaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatcatatattta -tatat-aatatatatcatatat-------------------------------------- -----------ttatatataaatatatatcatatatttatatataaatatatatcatatat -taatatatatcatatatttatatattaatatatatcatatatttatatattaatatatat -catatatttatatataaatatatatcatatatttatatataaatatatatctacattttt -tgagacagagtctggctctgtcaccccagctggagtgcagtggtacgatctcagctcatt -gcaacctccacctcccaggttcaagcgattctcgtgcctcagcctccatagtagctggaa -t diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7757219ce7f19ac23c5789d167c1c707.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7757219ce7f19ac23c5789d167c1c707.msa deleted file mode 100644 index fb485d2f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7757219ce7f19ac23c5789d167c1c707.msa +++ /dev/null @@ -1,145 +0,0 @@ ->syndip_1_chr20:61282406-61283769 -ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca -gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa -tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta -cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtattgtgttca -tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgca -tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg -cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg -tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg -catttgcacgcatgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg -tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg -cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgt-------------- ------------------------gtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc -gtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg----------- ------gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtg -cgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg -gcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgt -ttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcg -tgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttg -cacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgt -gtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac -gcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtg -atgtgtgtgcgtttgcacgcgtgtgc---------------------------------- --------------------------------------------------tgtgtgatgtg -tgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg -tggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgt -ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc -tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaat ->syndip_2_chr20:61282406-61283769 -ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca -gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa -tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta -cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttca -tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgca -tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg -cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg -tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg -catttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg -tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg -cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgt -gatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc -gcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgat -gtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtg -cgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg -gcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgt -ttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcg -tgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttg -cacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgt -gtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac -gcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtg -atgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcg -tgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgta -ggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctg -tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat -ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc -tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaat ->p:HG002_1_chr20:61282406-61283769 -ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca -gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa -tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta -cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttca -tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgtttagatgtgca -tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg -cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg -tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg -catttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg -tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg -cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgt -gatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc -gcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgat -gtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtg -cgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg -gcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgt -ttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcg -tgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttg -cacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgt -gtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac -gcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtg -atgtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcg -tgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgatgta -ggtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcgtttgcacgcgtgtgctg -tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat -ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc -tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaat ->p:HG002_2_chr20:61282406-61283769 -ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca -gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa -tctttggcatggtgtgtgtg--tgtgcatgtgtgtgtgtgtgtgtgtatgtctatctgta -cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtattgtgttca -tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcggatgtgca -tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg -cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg -tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg -catttgcacgcatgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg -tgtgtgatgtacgtgcatttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttg -cacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgt-------------- ------------------------gtgctgtggcgtgtgtgatgtacgtgcgtttgcacgc -gtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg----------- ------gtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtg -cgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtg -gcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcgt -ttgcacgcgtgttctgtggcgtgtgtgatgtacgtgcgtttgcacgcgtgtgctgtggcg -tgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttg -cacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgt -gtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac -gcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggcgtgtgtg -atgtgtgtgcgtttgcacgcgtgtgc---------------------------------- --------------------------------------------------tgtgtgatgtg -tgtgcgtttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg -tggtgtgtgatgtaggtgcatttgcacgcgtgtgctgtggtgtgtgtgatgtgtgtgcgt -ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc -tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaat ->ref_chr20:61282406-61283769 -ataaaacattctgtattttcaaaatgccaaaaaaattattgttaaagactttagaaaaca -gaaaagtacaaagaataaaagggtaacttcatttccctcctctgaacaaaccacttttaa -tctttggcatggtgtgtgtgcatgtgtgtgtgtgtgtgtgtgtgtgtatgtctatctgta -cttgtacctgcacacacaactggatgagcatggtgtgtgtgtacacatgtaatgtgttca -tatgtacatatgtgggtgccttgtgcacacgtgtgtggctgtgggatgttcagatgtgca -tgtgagttggtgtgtgtgcatgcccacaagcatgcatgtaaatgtgatgtgctgtgtatg -cacacggataagcatgtgtgaaggagtgcatgagagtggtgcatggctgtggtgtgcacg -tgtgtgcgtgtgatgcatgtgcatttgcacgcatgtgctgtggtgtgtgtgatgtacgtg -catttgcacgcgtgtgctgtggcgtgtgtgatgtacgtgcatttgcacgcgtgtgctgtg ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------gcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg----------- ------gcgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtg -cgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtg -gcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgt -ttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcg -tgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttg -cacgcgcgtgctgtggcgtgtgtgatgtacgtgcgtttgcacgcgcgtgctgtggc---- ------gtgtgtgcgtttgcacgcgcgtgctgtggcgtgtgtgatgtgtgtgcgtttgcac -gcgtgtgctgtggcgtgtgtgatgtgtgtgcgtttgcacgcgtgtgctgtggtgtgtgtg -atgtgtgtgcgtttgcacgcgtgtgc---------------------------------- ---------------------------------------------tgtggtgtgtgatgta -ggtgcatttgcacgcgtgtgctgtggtgtgtgatgtaggtgcatttacacgcgtgtgctg -tggtgtgtgatgtaggtgcatttgcacgtgtgtgctgtggtgtgtgtgatgtgtgtgcat -ttgcacgtgtgtgctgtggtgtgtgtgtggtgagtggatgggaggatatttccagtgctc -tcctcctgggactgatgccatgatgaaaatctgtgtaaaccagacagcacatctctcatc -atttctttgtgatgggtcattagaagcaggattctgaat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_783ef04c1562bdfce45b91b59fe4d678.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_783ef04c1562bdfce45b91b59fe4d678.msa deleted file mode 100644 index 286d2d50..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_783ef04c1562bdfce45b91b59fe4d678.msa +++ /dev/null @@ -1,125 +0,0 @@ ->syndip_1_chr20:641736-642565 -atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct -gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc -cccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctgggggggggg -gcccagcgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctgggg -gggggaggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttg -cctggg-----------------------------ggggggaggcccagcgggggtggag -ttgcctgggggggggcccagcgggggtggagttgcctgggggggg-ggcccagcgggggt -ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg--gcccag -cgggggtggagttgcctgggg---------------------------gggggaggccca -gcgggggtggagttgcctgggggggg-------------------------------ggc -ccagcgggggtggagttgcctg-gggggg---ggcccagcgggggtggagttgcctgggg -gggg---cccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctg --gggggggccccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagtt -gcctgggggggg--gcccagcgggggtggagttgcctggggggggcccagcgggggtgga -gttgcctggggggggccccagcgggggtggagttgcctgggggggggcccagcgggggtg -gagttgcctggggggggggcccagcgggggtggagttgcctggggggggggcccagcggg -ggtggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggggcccag -cgggggtggagttgcctg-gggggggggcccagcgggggtggagttgcct-ggggggggc -ccagcgggggtggagttgcct-gggggggggcccagcgggggtggagttgcctg-ggggg -ggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgtg -ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct -gggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag -gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg -tcgggcggggggcggcgctcgcagttccggagggg ->syndip_2_chr20:641736-642565 -atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct -gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc -cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg -gcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctgggg -gggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttg -cctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggag -ttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggt -ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccag -cgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggccca -gcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggggggaggc -ccagcgggggtggagttgcctg-ggggggggaggcccagcgggggtggagttgcctgggg -gggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcctg --ggggggg-cccagcgggggtggggttgcctggggggggaggcccagcaggggtggagtt -gcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtgga -gttgcctgggggggg-cccagcgggggtggagttgcctgggggggggcccagcggggatg -gggttgcct-gggggggggcccagcgggggtggggttgcct-gggggggggcccagcggg -ggtggagttgcct--gggggggggcccagcgggggtggagttgcct-ggggggggcccag -cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctgggggggggc -ccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgtggtgg -ggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgtg -ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct --ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag -gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg -tcgggcggggggcggcgctcgcagttccggagggg ->p:HG002_1_chr20:641736-642565 -atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct -gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc -cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg -gcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctgggg -gggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttg -cctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggag -ttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggt -ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccag -cgggggtggagttgcctgggggggggcccagcgggggtggagttgcctggggggggccca -gcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggggggaggc -ccagcgggggtggagttgcctg-ggggggggaggcccagcgggggtggagttgcctgggg -gggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtggggttgcctg --ggggggg-cccagcgggggtggggttgcctggggggggaggcccagcaggggtggagtt -gcctgggggggggtgcccagcgggggtggagttgcctggggggggcccagcgggggtgga -gttgcctgggggggg-cccagcgggggtggagttgcctgggggggggcccagcggggatg -gggttgcct-gggggggggcccagcgggggtggggttgcct-gggggggggcccagcggg -ggtggagttgcct--gggggggggcccagcgggggtggagttgcct-ggggggggcccag -cgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctgggggggggc -ccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgtggtgg -ggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgcctgtg -ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct --ggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag -gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg -tcgggcggggggcggcgctcgcagttccggagggg ->p:HG002_2_chr20:641736-642565 -atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct -gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc -cccccaatctggttgcctgggaggggggcccagcgggggtggagttgcctgggggggggg -gcccagcgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctgggg -gggggaggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttg -cctggg-----------------------------ggggggaggcccagcgggggtggag -ttgcctgggggggggcccagcgggggtggagttgcctgggggggg-ggcccagcgggggt -ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg--gcccag -cgggggtggagttgcctgggg---------------------------gggggaggccca -gcgggggtggagttgcctgggggggg-------------------------------ggc -ccagcgggggtggagttgcctg-gggggg---ggcccagcgggggtggagttgcctgggg -gggg---cccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctg --gggggggccccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagtt -gcctgggggggg--gcccagcgggggtggagttgcctggggggggcccagcgggggtgga -gttgcctggggggggccccagcgggggtggagttgcctgggggggggcccagcgggggtg -gagttgcctggggggggggcccagcgggggtggagttgcctggggggggggcccagcggg -ggtggagttgcctgggggggggggcccagcgggggtggagttgcctgggggggggcccag -cgggggtggagttgcctg-gggggggggcccagcgggggtggagttgcct-ggggggggc -ccagcgggggtggagttgcct-gggggggggcccagcgggggtggagttgcctg-ggggg -ggggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgcctgtg -ggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcct -gggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgcgggag -gcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacacggctg -tcgggcggggggcggcgctcgcagttccggagggg ->ref_chr20:641736-642565 -atcatccggtgacagggatcatcatccctgcctggcatagaaacccggacatcggaccct -gccctcccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgc -cccccaatctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggg -gcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctgggg -gggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttg -cctggggggggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggag -ttgcct-ggggggggcccagcgggggtggggttgcctggggggggaggcccagcgggggt -ggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggggtgcccag -cgggggtggagttgcct------------------------------------------- ---------------------gggggg-------------------------------ggc -ccagcgggggtggagttgcctgtggtggg---gggccagcgggggtgaagttgcctgggg -gggg----ccagcgggggtggagttgcctgggggggggccagcgggggtggagttgcctg -tgggggggggccagcgggggtggagttgcctgggggggg----ccagcgggggtggagtt -gcctgggggggg----ccagcgggggtggagcaccctggacggcccc--------gcgga -gccccctgcgggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaag -acattacacggctgtcgggcggggggcggcgctcgcagttccggagggg----------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7a1414e7f0509c4e857971aaf832e093.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7a1414e7f0509c4e857971aaf832e093.msa deleted file mode 100644 index c2ece0d5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7a1414e7f0509c4e857971aaf832e093.msa +++ /dev/null @@ -1,130 +0,0 @@ ->syndip_1_chr20:48449604-48450562 -ccatgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatct -gtgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtgga -ataggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggat -ggatggatggggtgggatgggatgggatg-----ggatggatggatgggatggatggatg -ggatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggat -gggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaa -tgggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgg -atggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatggga -tgggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggat -gggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatgga -tggat-----------------------ggatgggatgggatggatggatgggatgggat -gggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatg -gatgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggat -ggggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatgg -gatgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatga -gatgggatggatggcatgggatgggatgggattggatggggtgggatgggatggggtagg -atgggatgggatgggatgggatgggatgggatgggatgggatgggatggggtgggatggg -ttgggatgggatggggtgggttgggatggggtggggtgggatgggatgggatgggatggg -gtggggtggggtggggtgggatggggtgggatggggtgggatgggatggggtgggatggg -atgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggg -atgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggg -attggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggt -gggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaa -aatataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcat -ggacaaagcacttaaaaccacacagt ->syndip_2_chr20:48449604-48450562 -ccatgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatct -gtgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtgga -ataggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggat -ggatggatggggtgggatgggatgggatg-------------ggatggggtggatggatg -ggatgggataggatggatggggtgagatgggatggaatggatggaatgggatggatggat -gggatgggatggatgggatgggatggatgggatggatgggatgggatggatgggatggaa -tgggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgg -atggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatggga -tgggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggat -gggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatgga -tggatggatgggatgggatggatggatgggatgggatgggatggatggatgggatgggat -gggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatg -gatgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggat -ggggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatgg -gatgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatga -gatgggatggatggcatgggatggaatgggattggatggggtgggatgggatggggtagg -atgggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatggg -gtgggttgggatgggg----------tggggtgggatgggatgggatggggtgggatggg -gtgggatggggtgggatggggtgggatgggatggggtgggatgggatgggatgggatggg -gtgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggg -atgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggg -attggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggt -gggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaa -aatataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcat -ggacaaagcacttaaaaccacacagt ->p:HG002_1_chr20:48449604-48450562 -ccatgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatct -gtgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtgga -ataggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggat -ggatggatggggtgggatgggatgggatg-------------ggatggggtggatggatg -ggatgggataggatggatggggtgagatgggatggaatggatggaatgggatggatggat -gggatgggatggatgggatgggatggatgggatggatgggatgggatggatgggatggaa -tgggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgg -atggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatggga -tgggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggat -gggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatgga -tggatggatgggatgggatggatggatgggatgggatgggatggatggatgggatgggat -gggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatg -gatgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggat -ggggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatgg -gatgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatga -gatgggatggatggcatgggatggaatgggattggatggggtgggatgggatggggtagg -atgggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatggg -gtgggttgggatgggg----------tggggtgggatgggatgggatggggtgggatggg -gtgggatggggtgggatggggtgggatgggatggggtgggatgggatgggatgggatggg -gtgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggg -atgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggg -attggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggt -gggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaa -aatataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcat -ggacaaagcacttaaaaccacacagt ->p:HG002_2_chr20:48449604-48450562 -ccatgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatct -gtgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtgga -ataggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggat -ggatggatggggtgggatgggatgggatg-----ggatggatggatgggatggatggatg -ggatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggat -gggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaa -tgggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgg -atggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatggga -tgggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggat -gggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatgga -tggat-----------------------ggatgggatgggatggatggatgggatgggat -gggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatg -gatgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggat -ggggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatgg -gatgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatga -gatgggatggatggcatgggatgggatgggattggatggggtgggatgggatggggtagg -atgggatgggatgggatgggatgggatgggatgggatgggatgggatggggtgggatggg -ttgggatgggatggggtgggttgggatggggtggggtgggatgggatgggatgggatggg -gtggggtggggtggggtgggatggggtgggatggggtgggatgggatggggtgggatggg -atgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggg -atgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggg -attggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggt -gggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaa -aatataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcat -ggacaaagcacttaaaaccacacagt ->ref_chr20:48449604-48450562 -ccatgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatct -gtgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtgga -ataggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggat -ggatggatggggtgggatgggatgggatgggatgggatggatggatgggatggatggatg -ggatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggat -gggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaa -tgggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgg -atggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatggga -tgggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggat -gggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatgga -tggat-----------------------ggatgggatgggatggatggatgggatgggat -gggatggggtggatgggatggatggatggatgggatgggatggatggatgggatgggat- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------gg -atgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggg -attggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggt -gggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaa -aatataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcat -ggacaaagcacttaaaaccacacagt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7a6fa948b255c8d7baeb998b681ef296.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7a6fa948b255c8d7baeb998b681ef296.msa deleted file mode 100644 index fc8f9768..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7a6fa948b255c8d7baeb998b681ef296.msa +++ /dev/null @@ -1,120 +0,0 @@ ->syndip_1_chr20:641802-642530 -ccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgcccccca -atctggttgcctgggacgggggcccagcgggggtggagttgcctgggggggggggcccag -cgggggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctggg -ggggggaggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagtt -gcct--ggggggggcccagcgggggtggagttgcct-gtggggggaggcccagcgggggt -ggagttgcctgggggg----ggcccagcgggggtggggttgcct-ggggggggaggccca -gcgggggtggagttgcctgggggggggaggcccagcgggggtggagttgcctgggggggg -gtgcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctgtggt -gg-ggggccagcgggggtgaagttgcctgggggggg-----ccagcgggggtggagttgc -ctggggggggg---ccagcgggggtggagttgcctgggggggggcccagcgggggtggag -ttgcctgggggggggccagcgggggtggagttgcctgggggggg----ccagcgggggtg -gagttgcct--gggggggggcccagcgggggtggagttgcctggggggggggcccagcgg -gggtggagttgcctgggggggg-ggcccagcgggggtggagttgcctggg---------- --------------------ggggggggcccagcgggggtggagttgcctgggggggggcc -cagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgggggggg -cccagcgggggtggagttgcctg-ggggggggc--------------------------- ------ccagcgggggtggagttgcctgggggggg-------------------------- --------ggcccagcgggggtggagttgcctg-gggggggcccagcgggggtggagttgc -ctgtgggggggggcccagcgggggtggagttgcctggggggggcccagcgggggtggagt -tgcctgggggggggcccagcgggggtggagcaccctggacggccccgcggagccccctgc -gggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacac -ggctg ->syndip_2_chr20:641802-642530 -ccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgcccccca -atctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggggcccag -cgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttgcctggg -ggg----ggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggagtt -gcct--ggggggggcccagcgggggtggggttgcct-ggggggggaggcccagcgggggt -ggagttgcctgggggggggaggcccagcgggggtggagttgcct-gggggggggtgccca -gcgggggtggagttgcctggggggg---ggcccagcgggggtggagttgcctggggggg- ---gcccagcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggg -gggaggcccagcgggggtggagttgcctgggggggggaggcccagcgggggtggagttgc -ctgggggggggtgcccagcgggggtggagttgcct-ggggggggcccagcgggggtgggg -ttgcctggggggggcccagcgggggtggggttgcctggggggggaggcccagcaggggtg -gagttgcctgggggggggtgcccagcgggggtggagttgcct--ggggggggcccagcgg -gggtggagttgcctgggggg---ggcccagcgggggtggagttgcctgggggggggccca -gcggggatggggttgcctgggggggggcccagcgggggtggggttgcctgggggggggcc -cagcgggggtggagttgcctgggggggg-gcccagcgggggtggagttgcctgggggggg -cccagcgggggtggagttgcctgtggtgggggg-ccagcgggggtgaagttgcctggggg -ggg--ccagcgggggtggagttgcctggggggggggcccagcgggggtggagttgcctgt -ggtggggggcccagcgggggtggagttgcctgtgggggggcccagcgggggtggagttgc -ctgtggggggggg-ccagcgggggtggagttgcctgggggggg-ccagcgggggtggagt -tgcctgggggggg--ccagcgggggtggagcaccctggacggccccgcggagccccctgc -gggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacac -ggctg ->p:HG002_1_chr20:641802-642530 -ccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgcccccca -atctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggggcccag -cgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttgcctggg -ggg----ggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggagtt -gcct--ggggggggcccagcgggggtggggttgcct-ggggggggaggcccagcgggggt -ggagttgcctgggggggggaggcccagcgggggtggagttgcct-gggggggggtgccca -gcgggggtggagttgcctggggggg---ggcccagcgggggtggagttgcctggggggg- ---gcccagcgggggtggggttgcctggggggggcccagcgggggtggggttgcctggggg -gggaggcccagcgggggtggagttgcctgggggggggaggcccagcgggggtggagttgc -ctgggggggggtgcccagcgggggtggagttgcct-ggggggggcccagcgggggtgggg -ttgcctggggggggcccagcgggggtggggttgcctggggggggaggcccagcaggggtg -gagttgcctgggggggggtgcccagcgggggtggagttgcct--ggggggggcccagcgg -gggtggagttgcctgggggg---ggcccagcgggggtggagttgcctgggggggggccca -gcggggatggggttgcctgggggggggcccagcgggggtggggttgcctgggggggggcc -cagcgggggtggagttgcctgggggggg-gcccagcgggggtggagttgcctgggggggg -cccagcgggggtggagttgcctgtgggggggggcccagcgggggtggagttgcctggggg -ggggcccagcgggggtggagttgcctgtggtggggggccagcgggggtgaagttgcctg- ----gggggggccagcgggggtggagttgcctg-ggggggggccagcgggggtggagttgc -ctgtggggggggg-ccagcgggggtggagttgcctgggggggg-ccagcgggggtggagt -tgcctgggggggg--ccagcgggggtggagcaccctggacggccccgcggagccccctgc -gggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacac -ggctg ->p:HG002_2_chr20:641802-642530 -ccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgcccccca -atctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggggcccag -cgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctgggggggg--gcccagcgggggtggagttgcctggg -ggggggaggcccagcgggggtggagttgcctg--ggggggggcccagcgggggtggagtt -gcctggggggggggcccagcgggggtggagttgcctgggggggggaggcccagcgggggt -ggagttgcctggggggg---ggcccagcgggggtggagttgcctgggggggggaggccca -gcgggggtggagttgcctgggggggg--ggcccagcgggggtggagttgcctgggggggg ---gcccagcgggggtggagttgcctggggggggcccagcgggggtggagttgcctggggg ----gggcccagcgggggtggagttgcctgggggggg---ccccagcgggggtggagttgc -ctggggggggg--cccagcgggggtggagttgcctgggggggggcccagcgggggtggag -ttgcctggggggtgcccagcgggggtggagttgcctgggggggg---cccagcgggggtg -gagttgcctgtggggggaggcccagcgggggtggagttgcct--ggggggggcccagcgg -gggtggggttgcctggggggggaggcccagcgggggtggagttgcctggg---------- -------------------ggggggaggcccagcgggggtggagttgcctgggggggggcc -cagcgggggtggagttgcctggggggggtgcccagcgggggtggagttgcctgggggggg -cccagcgggggtggagttgcctgtggtgggggg--------------------------- ------ccagcgggggtgaagttgcctgggggggg-------------------------- -----------ccagcgggggtggagttgcctg-ggggggggccagcgggggtggagttgc -ctgtggggggggg-ccagcgggggtggagttgcctgggggggg-ccagcgggggtggagt -tgcctgggggggg--ccagcgggggtggagcaccctggacggccccgcggagccccctgc -gggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacac -ggctg ->ref_chr20:641802-642530 -ccgctgcttccgcagggacagggggcagccagcagagcctccctctgggggtgcccccca -atctggttgcctgggacgggggcccagcgggggtggagttgcct-ggggggggggcccag -cgggggtggagttgcctggggggggaggcccagcgggggtggagttgcctggggggggga -ggcccagcgggggtggagttgcctgggggggggtgcccagcgggggtggagttgcctggg -ggg----ggcccagcgggggtggagttgcctgtggggggaggcccagcgggggtggagtt -gcct--ggggggggcccagcgggggtggggttgcct-ggggggggaggcccagcgggggt -ggagttgcctgggggggggaggcccagcgggggtggagttgcct-gggggggggtgccca -gcgggggtggagttgcct------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------gggggggg -cccagcgggggtggagttgcctgtggtgggggg--------------------------- ------ccagcgggggtgaagttgcctgggggggg-------------------------- -----------ccagcgggggtggagttgcctg-ggggggggccagcgggggtggagttgc -ctgtggggggggg-ccagcgggggtggagttgcctgggggggg-ccagcgggggtggagt -tgcctgggggggg--ccagcgggggtggagcaccctggacggccccgcggagccccctgc -gggaggcgagggcggccctcgggctctggaaggggccgcgcggcctggaagacattacac -ggctg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7a81221a23ca83388f8ff376debbd4cc.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7a81221a23ca83388f8ff376debbd4cc.msa deleted file mode 100644 index 04fcd3ce..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7a81221a23ca83388f8ff376debbd4cc.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:16395048-16395522 -tacagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcgg -tgtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaa -aggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggaga -ggaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggagg -ccaagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagg -agaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggagg -ggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggaga -agatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttccttt -catataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggctttt -ggtattcaaa ->syndip_2_chr20:16395048-16395522 -tacagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcgg -tgtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaa -aggagatgaggaaggggagaggaggggagaggaggggag--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------gggaggggaggggagaggaggggaggccaagggaga -agatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttccttt -catataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggctttt -ggtattcaaa ->p:HG002_1_chr20:16395048-16395522 -tacagtcatggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcattgg -tgtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtccaggcagaa -aggagatgaggaaggggagaggaggggagaggaggggag--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------gggaggggaggggagaggaggggaggccaagggaga -agatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttccttt -catataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggctttt -ggtattcaaa ->p:HG002_2_chr20:16395048-16395522 -tacagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcgg -tgtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaa -aggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggaga -ggaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggagg -ccaagggaggggaggggaggggaggagaggggaggccaagggaggggaggggaggggagg -agaggggaggccaagggaggggaggggaggagaggggaggccaagggaggggaggggagg -ggaggagaggggaggccaagggaggggaggggaggggaggagaggggaggccaagggaga -agatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttccttt -catataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggctttt -ggtattcaaa ->ref_chr20:16395048-16395522 -tacagtcgtggacagcaaagctaaggctcagtacaacaaagggcatacccctgtcatcgg -tgtcttcttactctctccctaatgtgatgtattcatcctcccagtttagtcaaggcagaa -aggagatgaggaaggggagaggaggggagaggagggaagaggaggggaggggaggggaga -ggaggagaggggaggagaggggaggccaagggaggggaggggaggggaggagaggggagg -ccaa-----gggaggggaggggaggagaggggaggccaagggaggggaggggaggggagg -agaggggaggccaa---------------------------------------------- -------------------------gggaggggaggggaggagaggggaggccaagggaga -agatatgaaagaaatagggaaggagtgggacacagggaggaaaacaaaactatttccttt -catataaatgttgtcatctggggagaagccctcactatctccttggtgcctttggctttt -ggtattcaaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7ac3ce17505493fab61a6ea8ba3747a6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7ac3ce17505493fab61a6ea8ba3747a6.msa deleted file mode 100644 index 9de935b3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7ac3ce17505493fab61a6ea8ba3747a6.msa +++ /dev/null @@ -1,195 +0,0 @@ ->syndip_1_chr20:55943818-55945908 -tgtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctcctt -ccaagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttc -agccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtgga -tcacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctact -aaaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggag -gctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggca -ccactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatat -atatatagatacacacacacacacacacacacacac------------------------ -----------atatatatatatatatatatatatatatatatatgcatgcatgccagatg -cagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgag -gtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaataca -aaattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcag -gagaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcact -ccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatct -atagatatatatctagatatagatctatgagtatatatctatagatatctagatatatat -ttatagatagatatatctatagatatctatatatttctatcgatagagatatctatagat -atctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacat -agatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatt -ttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagata -gtatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctaga -tatct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatcta -gatatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagat -atctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctat -ctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgt -cgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagt -atctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatcta -gatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatc -tatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagta -tctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctg -tctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctg -tctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaac -tgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatga -ggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccc -atgggc ->syndip_2_chr20:55943818-55945908 -tgtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctcctt -ccaagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttc -agccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtgga -tcacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctact -aaaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggag -gctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggca -ccactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatat -atatatagatacacacacacacacacacacacacacacacacacacacacacacacatat -atatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatg -cagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgag -gtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaataca -aaattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcag -gagaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcact -ccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatct -atagatatatatctagatatagatctatgagtatatatctatagatatctagatatatat -ttatagatagatatatctatagatatctatatatttctatcgatagagatatctatagat -atctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacat -agatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatt -ttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagata -gtatctatctagatatcgg--------------------tctagatagtatctatctaga -tatctgcgtagatgtctagatatctatctagatat---------------tatctatcta -ga---------------------------------------------------------- ------------------------------------------tatctgtcgctatctagat -atctatctaga---tatctgtcgctatctagatatctatctaga---------------- ------------------------------------------------------tatctgt -cgctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatc -atctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatctatcta -gatatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatc -tatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagta -tctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctg -tctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctg -tctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaac -tgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatga -ggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccc -atgggc ->p:HG002_1_chr20:55943818-55945908 -tgtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctcctt -ccaagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttc -agccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtgga -tcacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctact -aaaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggag -gctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggca -ccactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatat -atatatagatacacacacacacacacacacacacacacacacacacacacacacacatat -atatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatg -cagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgag -gtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaataca -aaattagctggctgtggtggctcatgctggtaattccagctacttgggaggctgaggcag -gagaatcacatgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcact -ccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatct -atagatatatatctagatatagatctatgagtatatatctatagatatctagatatatat -ttatagatagatatatctatagatatctatatatttctatcgatagagatatctatagat -atctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacat -agatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatt -ttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagata -gtatctatctagatatcgg--------------------tctagatagtatctatctaga -tatctgcgtagatgtctagatatctatctagatat---------------tatctatcta -ga---------------------------------------------------------- ------------------------------------------tatctgtcgctatctagat -atctatctaga---tatctgtcgctatctagatatctatctaga---------------- ------------------------------------------------------tatctgt -cgctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatc -atctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatctatcta -gatatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatc -tatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagta -tctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctg -tctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctg -tctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaac -tgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatga -ggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccc -atgggc ->p:HG002_2_chr20:55943818-55945908 -tgtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctcctt -ccaagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttc -agccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtgga -tcacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctact -aaaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggag -gctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggca -ccactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatat -atatatagatacacacacacacacacacacacacac------------------------ -----------atatatatatatatatatatatatatatatatatgcatgcatgccagatg -cagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgag -gtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaataca -aaattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcag -gagaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcact -ccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatct -atagatatatatctagatatagatctatgagtatatatctatagatatctagatatatat -ttatagatagatatatctatagatatctatatatttctatcgatagagatatctatagat -atctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacat -agatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatt -ttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagata -gtatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctaga -tatct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatcta -gatatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctat -ctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagat -atctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctat -ctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgt -cgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagt -atctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatcta -gatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatc -tatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagta -tctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctg -tctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctg -tctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaac -tgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatga -ggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccc -atgggc ->ref_chr20:55943818-55945908 -tgtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctcctt -ccaagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttc -agccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtgga -tcacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctact -aaaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggag -gctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggca -ccactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatat -atatatagatacacacacacacacacacacacacac------------------------ -----------atatatatatatatatatatatatatatatatatgcatgcatgccagatg -cagtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgag -gtcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaataca -aaattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcag -gagaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcact -ccagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatct -atagatatatatctagatatagatctatgagtatatatctatagatatctagatatatat -ttatagatagatatatctatagatatctatatatttctatcgatagagatatctatagat -atctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacat -agatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacatt -ttttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagata -gtatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctaga -tatct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatcta -ga---------------------------------------------------------- ------------------------------------------tatctgtcgctatctagat -atctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctat -ctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgt -cgctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagt -atctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatcta -gatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatc -tatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatcta -gatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgc -tatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatc -tgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagta -tctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctg -tctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctg -tctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaac -tgccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatga -ggtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccc -atgggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7ca10eb32dd50e600280f16b4afb82f5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7ca10eb32dd50e600280f16b4afb82f5.msa deleted file mode 100644 index 7f787dda..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7ca10eb32dd50e600280f16b4afb82f5.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:57948698-57949590 -cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt -tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg -ccctgcacagatggacagatggttggaa----ggatggatggatggatggatggatggat -ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt -ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat -ggatt----------------gatggatggatggatggatggatggatggaagaatggat -gatggatggatga--------------------gatggatggatggatggatggaagaat -ggatgatggatggatga--------gatggatggatggatggggggttggatggatggat -gg------------------------------------------------------atgg -atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat -gaatggatgatggatggatgaatgagatggatggatt------------gatggatggat -ggatggatggaagaatggatgatggatggatgaatgagatgggtggattgatggatggat -ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag -gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg ->syndip_2_chr20:57948698-57949590 -cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt -tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg -ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat -ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt -ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat -ggattgatggatggatggatggatggatggatggatggatggatggatggaagaatggat -gatggatggatgagatggatggatggatggatggatggatggatggatggatggaagaat -ggatgatggatggatgagatggatggatggatggatggatggggggttggatggatggat -ggatggatggatggatagtggatagatggatgaatagtgaatggataaatggattaatgg -atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat -gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat -ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat -ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag -gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg ->p:HG002_1_chr20:57948698-57949590 -cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt -tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg -ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat -ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt -ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat -ggattgatggatggatggatggatggatggatggatggatggatggatggaagaatggat -gatggatggatgagatggatggatggatggatggatggatggatggatggatggaagaat -ggatgatggatggatgagatggatggatggatggatggatggggggttggatggatggat -ggatggatggatggatagtggatagatggatgaatagtgaatggataaatggattaatgg -atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat -gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat -ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat -ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag -gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg ->p:HG002_2_chr20:57948698-57949590 -cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt -tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg -ccctgcacagatggacagatggttggaa----ggatggatggatggatggatggatggat -ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt -ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat -ggatt----------------gatggatggatggatggatggatggatggaagaatggat -gatggatggatga--------------------gatggatggatggatggatggaagaat -ggatgatggatggatga--------gatggatggatggatggggggttggatggatggat -gg------------------------------------------------------atgg -atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat -gaatggatgatggatggatgaatgagatggatggatt------------gatggatggat -ggatggatggaagaatggatgatggatggatgaatgagatgggtggattgatggatggat -ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag -gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg ->ref_chr20:57948698-57949590 -cggagcgggtgtgccccgtggtctctcttcactgttcttaagacattcacaacctcattt -tgatggtgggacgctgcagctcacgtctgagtcccatccaagacttggcccactgctgtg -ccctgcacagatggacagatggttggaaggatggatggatggatggatggatggatggat -ggatggggttggatggatggatggatggatggatggatagtggatagatggatgaatagt -ggatggataaatggattaatggatggatgaatggatgatggatggatgaatgagatggat -ggattgatggatggatggatggatggatggatggatggatggatggatggaagaatggat -gatggatggatgagatggatggatggatggatggatggatggatggatggatggaagaat -ggatgatggatggatgagatggatggatggatggatggatggggggttggatggatggat -ggatggatggatggatagtggatagatggatgaatagtgaatggataaatggattaatgg -atggatggatagtggatagatggatgaatagtggatggataaatggattaatggatggat -gaatggatgatggatggatgaatgagatggatggattgatggatggatggatggatggat -ggatggatggaagaatggatgatggatggatgaatgagatgggtggatt----gatggat -ggatggatggatggatggatggatggatggatggcagatggatggatccatctatgtcag -gcctgcatgacacctggtgtggaggagccacccagtcaacatttgctgacaggatggaca -gacagagaggaggtgagtgacaggggccctcaggtgctttttctttggagacctggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7ca72f6037601dfb2d223be9e9e50717.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7ca72f6037601dfb2d223be9e9e50717.msa deleted file mode 100644 index bf049a1e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7ca72f6037601dfb2d223be9e9e50717.msa +++ /dev/null @@ -1,35 +0,0 @@ ->syndip_1_chr20:10802617-10802954 -atctgcaaagatctaattttcaaatgaggtcacagtcacaagtattgggggttaggactt -ttgggggacataacccacaatgtcctctgaatatatatatatatatcctcccatatatat -atatatcctcccatatatatatatatat-------------------------------- -------------------------------------------------atatatatatat -atatcctcccatatatatatatatcctcccatatatatatctatcctcccatatatatat -atatatatatattttcaatgtatccctttattcaagtg ->syndip_2_chr20:10802617-10802954 -atctgcaaagatctaattttcaaatgaggtcacagtcacaagtattgggggttaggactt -ttgggggacataacccacaatgtcctctgaatatatatatatatatcctcccatatatat -atatatatatatatatcctcccatatatatatatatatatatatatatcctcccatatat -atatatatatatatatcctcccatatatatatatatatatgtcctcccatatatatatat -atatcctcccatatatatatatatcctcccatatatatatctatcctcccatatatatat -atatatatatattttcaatgtatccctttattcaagtg ->p:HG002_1_chr20:10802617-10802954 -atctgcaaagatctaattttcaaatgaggtcacagtcacaagtattgggggttaggactt -ttgggggacataacccacaatgtcctctgaatatatatatatatatcctcccatatatat -atatatatatatatatcctcccatatatatatatatatatatatatatcctcccatatat -atatatatatatatatcctcccatatatatatatatatatgtcctcccatatatatatat -atatcctcccatatatatatatatcctcccatatatatatctatcctcccatatatatat -atatatatatattttcaatgtatccctttattcaagtg ->p:HG002_2_chr20:10802617-10802954 -atctgcaaagatctaattttcaaatgaggtcacagtcacaagtattgggggttaggactt -ttgggggacataacccacaatgtcctctgaatatatatatatatatcctcccatatatat -atatatatatatatatcctcccatatat-------------------------------- -------------------------------------------------atatatatatat -atatcctcccatatatatatatatcctcccatatatatatctatcctcccatatatatat -atatatatatattttcaatgtatccctttattcaagtg ->ref_chr20:10802617-10802954 -atctgcaaagatctaattttcaaatgaggtcacagtcacaagtattgggggttaggactt -ttgggggacataacccacaatgtcctctgaatatatatatatatatcctcccatatatat -atatatatatatatatcctcccatatatatatatatatatatatatatcctcccatatat -atatatatatatatatcctcccatatatatatatatatatgtcctcccatatatatatat -atatcctcccatatatatatatatcctcccatatatatatctatcctcccatatatatat -atatatatatattttcaatgtatccctttattcaagtg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_7d4315446a621c1d4a1d8ccb36fdb130.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_7d4315446a621c1d4a1d8ccb36fdb130.msa deleted file mode 100644 index f1266eda..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_7d4315446a621c1d4a1d8ccb36fdb130.msa +++ /dev/null @@ -1,60 +0,0 @@ ->syndip_1_chr20:63154485-63155095 -gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc -ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc -cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct -tcctcctccctcctcttc------------------------------------------ ---------------cctccctcctgcttcctccctctgccctccctcctccctcttcctc -cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc -caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca ----------------------tcccttcctcctcctccctccttcctccctcctccctcc -tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca -gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaatt ->syndip_2_chr20:63154485-63155095 -gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc -ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc -cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct -tcctcctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctctt -cctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctcttcctc -cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc -caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca -tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc -tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca -gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaatt ->p:HG002_1_chr20:63154485-63155095 -gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc -ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc -cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct -tcctcctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctctt -cctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctcttcctc -cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc -caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca -tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc -tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca -gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaatt ->p:HG002_2_chr20:63154485-63155095 -gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc -ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc -cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct -tcctcctccctcctcttc------------------------------------------ ---------------cctccctcctgcttcctccctctgccctccctcctccctcttcctc -cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc -caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca ----------------------tcccttcctcctcctccctccttcctccctcctccctcc -tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca -gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaatt ->ref_chr20:63154485-63155095 -gaagagggagatggactggcctcagccaccccggagtacagggatgtcatcacaccagcc -ctccagcggctgaaagagccagtgagaggcaggtgggggtgtggatcaggcctgatctcc -cctagtctcctcctgcaatgcccagattcttgcccccgtccttccttctccctcctccct -tcctcctccctcctcttccctccctcctgcttcctccctctgccctccctcctccctctt -cctccctcct----cctccttcctgcttcctccctctgccctccctcctccctcttcctc -cctcctcctcccctctcctctttcctcctccctctcccttcctcctcctcccccctttcc -caccctcctccccctttccctccctcctcccgactccctctccccttctccctcttctca -tcccttcctcctcctccctcctcccttcctcctcctccctccttcctccctcctccctcc -tccccacactgtccatttgcaggctgcctggtcctagcccatatccaagggcctgtctca -gctacaaagttctgctctctgcttttaaatgaggacacaaggtggtttccaaaacacatg -tacaaggcagaaatt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_804e97fd9987022249aab226ce9f5abb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_804e97fd9987022249aab226ce9f5abb.msa deleted file mode 100644 index acc39507..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_804e97fd9987022249aab226ce9f5abb.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:61201712-61202352 -tttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggt -gtcacctccatcctcactcaggacactccatggtgtcacctccatccttactcaggaccc -tccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcac -tcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg-gtgtcaccgc -catcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcccctgtaag -tgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc----ctcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcaccgccatcct -cactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctca--------------- --------------ccaggaccctccatgagtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactca -ggaccctccat-ggtgtcaccgccatcctca----------------------------- ---ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctcaccaggatcccctgta -agtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcactcagga -ccctccatggtgtcacctccatcctcactcaggaccctccata-gtgccacctccatcct -cac-caggatcccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtca -cctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatgggtgtcacctccatcctcac-tcaggaccctccatggtgtcacctccatc -ctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc -catggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactc -aggaccctccatg------------------------------------gtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtg -tcacc---------------------------------- ->syndip_2_chr20:61201712-61202352 -tttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggt -gtcacctccatcctcactcaggacactccatggtgtcacctccatccttactcaggaccc -tccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcac --caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctc -catcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatgg -tgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcaccgccatcct -cactcaggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcac -ctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccctccatgagt -gtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactca -ggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtgtcacctcca -tcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat -ggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttactcagga -ccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcct -cac-caggatcccctgtaagtgtcacctccatcctcactcaggaccctccatgagtgtca -cctccatcctca----ggaccctccatggtgtcacctccatcctca---ggaccctccat -gagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatc -ctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatg-gtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacactc -catggtgtcacctccatccttactcaggaccctccat-ggtgtcaccgccatcctcactc -aggaccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccatggtgtcacc ->p:HG002_1_chr20:61201712-61202352 -tttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggt -gtcacctccatcctcactcaggacactccatggtgtcacctccatccttactcaggaccc -tccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcac --caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctc -catcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatgg -tgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactcaggac -cctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcct -cactcaggaccctccatgggtgccacctccatcctcaccaggatcccctgtaagtgtcac -ctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccctccatgagt -gtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactca -ggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtgtcacctcca -tcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccat -ggtgtcacctccatcctcactcggaccctccatgagtgtcacctccatcctcactcagga -ccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcct -cac-caggatcccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtca -cctccatcctca----ggaccctccatggtgtcacctccatcctca---ggaccctccat -gagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatc -ctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatg-gtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggacactc -catagtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactc -aggaccctccatg-gtgtcacctccatcctcactcaggaccctccatgggtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtg -tcacctccatcctcactcaggaccctccatggtgtcacc ->p:HG002_2_chr20:61201712-61202352 -tttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggaccctccatggt -gtcacctccatcctcactcaggacactccatggtgtcacctccatccttactcaggaccc -tccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcac --caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctc -catcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcccctgtaag -tgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc----ctcaggac -cctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccatcct -cactcaggaccctccatg-gtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctca--------------- --------------ccaggaccctccatgagtgtcacctccatcctcactcaggaccctcc -atggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactca -ggaccctccat-ggtgtcaccgccatcctca----------------------------- ---ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgtcac -ctccatcctcactcaggaccctccatggtgtcacctccatcctcaccaggatcccctgta -agtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcactcagga -ccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcct -cac-caggatcccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtca -cctccatcctcactcaggaccctccatggtgtcacctccatcctcactcggaccctccat -gagtgtcacctccatcctcactcaggaccctccatggtgtcaccgccatcctcactcagg -accctccatgagtgccacctccatcctcac-caggatcccctgtaagtgtcacctccatc -ctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc -catggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactc -aggaccctccatg------------------------------------gtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtg -tcacc---------------------------------- ->ref_chr20:61201712-61202352 -tttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggaccctccatg-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------gtgtcacctccatcctcactcagga -cactccatggtgtcacctccatccttactcaggaccctccatg-gtgtcaccgccatcct -cactcaggaccctccatgagtgccacctccatcctcac-caggatcccctgtaagtgtca -cctccatcctcaccaggaccctccatgagtgtcacctccatcctca---ggaccctccat -gagtgtcacctccatcctcactcaggaccctccatggtgtcaccgccatcctcactcagg -accctccatgagtgccacctccatcctcac-caggatcccctgtaagtgtcacctccatc -ctcac-caggaccctccatgagtgtcacctccatc----ctcaggaccctccatgagtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc -catggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctcactc -aggaccctccatg------------------------------------gtgtcacctcc -atcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtg -tcacc---------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_841314eefaf85faf44b7e1249b9ffe7e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_841314eefaf85faf44b7e1249b9ffe7e.msa deleted file mode 100644 index 53f36afa..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_841314eefaf85faf44b7e1249b9ffe7e.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:21721073-21721836 -gagtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgttt -tcttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgta -gaccacattggctattacatatatatatataatatatatgtaatatatatatgtaatgta -tattatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatata -tattatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtata -tatgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacat -atataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatata -taatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgta -tattatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtata -ttatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtat -tacatatataacatatatgtattacatatatgtattacatatataacatatatgtattac -atatatgtattacatatataacatatatgtaatacatatatgtattacatatataacata -tatgtattacatatatgtattacatatataacatatatgtattacatatatgtattacat -atataacatatatgtattacatatatgtattacatatataacatatatgtattacatata -tgtattacatatataacatatatgtattacatatatgtaatacatatataacatatatgt -attacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatata -acatatatgtattacatatatgtaatacatatataac----atgtattacatatatgtaa -tacatatataac--------------------------atgtattacatatatgtaatac -atatataacatgtattacatatatgtaatacacatataatatatatgttatatatatata -tatatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccagg -ctggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgat -cctcccacctcaacctcct ->syndip_2_chr20:21721073-21721836 -gagtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgttt -tcttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgta -gaccacattggctattacatatatatatataatatatatgtaatatatatatgtaatgta -tattatatatgtaatgtatataatatatgtaatgtatataatacatatgtaatacatata -tattatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtata -tatgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacat -atataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatata -taatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgta -tattatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtata -ttatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtat -tacatatataacatatatgtattacatatatgtattacatatataacatatatgtattac -atatatgtattacatatataacatatatgtattacatatatgtattacatatataacata -tatgtattacatatatgtattacatatataacatatatgtattacatatatgtattacat -atataacatatatgtattacatatatgtattacatatataacatatatgtattacatata -tgtattacatatataacatatatgtattacatatatgtattacatatataacatatatgt -attacatatatgtattacatatataacatatatgtattacatatatgtattacatatata -acatatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaa -tacatatataacatatatgtaatacatatataacatatatgtattacatatatgtaatac -atatataacatgtattacatatatgtaatacacatataatatatatgttatatatatata -tatatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccagg -ctggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgat -cctcccacctcaacctcct ->p:HG002_1_chr20:21721073-21721836 -gagtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgttt -tcttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgta -gaccacattggctattacatatatatatataatatatatgtaatatatatatgtaatgta -tattatatatgtaatgtatataatatatgtaatgtatataatacatatgtaatacatata -tattatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtata -tatgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacat -atataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatata -taatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgta -tattatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtata -ttatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtat -tacatatataacatatatgtattacatatatgtattacatatataacatatatgtattac -atatatgtattacatatataacatatatgtattacatatatgtattacatatataacata -tatgtattacatatatgtattacatatataacatatatgtattacatatatgtattacat -atataacatatatgtattacatatatgtattacatatataacatatatgtattacatata -tgtattacatatataacatatatgtattacatatatgtattacatatataacatatatgt -attacatatatgtattacatatataacatatatgtattacatatatgtattacatatata -acatatatgtattacatatatgtaatacatatataacatatatgtattacatatatgtaa -tacatatataacatatatgtaatacatatataacatatatgtattacatatatgtaatac -atatataacatgtattacatatatgtaatacacatataatatatatgttatatatatata -tatatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccagg -ctggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgat -cctcccacctcaacctcct ->p:HG002_2_chr20:21721073-21721836 -gagtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgttt -tcttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgta -gaccacattggctattacatatatatatataatatatatgtaatatatatatgtaatgta -tattatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatata -tattatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtata -tatgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacat -atataatatatatgtaatgtatatatatgtaatgtatataatatatatgtaatacatata -taatatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgta -tattatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtata -ttatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtat -tacatatataacatatatgtattacatatatgtattacatatataacatatatgtattac -atatatgtattacatatataacatatatgtaatacatatatgtattacatatataacata -tatgtattacatatatgtattacatatataacatatatgtattacatatatgtattacat -atataacatatatgtattacatatatgtattacatatataacatatatgtattacatata -tgtattacatatataacatatatgtattacatatatgtaatacatatataacatatatgt -attacatatatgtaatacatatataacatatatgtattacatatatgtaatacatatata -acatatatgtattacatatatgtaatacatatataac----atgtattacatatatgtaa -tacatatataac--------------------------atgtattacatatatgtaatac -atatataacatgtattacatatatgtaatacacatataatatatatgttatatatatata -tatatataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccagg -ctggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgat -cctcccacctcaacctcct ->ref_chr20:21721073-21721836 -gagtagggacttgctttgggtcacagtcagcttttattagtgttattattgttgctgttt -tcttctttttctttgtacatcaacgttttatggtgaattaaatcgtgttttaaccttgta -gaccacattggctattacatatatatatataatatatatgtaatatatatatgtaatgta -tattatatatgtaatgtatataatatatgtaatgtatataatatatatgtaatacatata -tattatatatgtatataatacatatatatgtatatatatgtatgtatatatatatgtata -tatgtatatatatatgtatataatacatatatatacatatatattatatatgtaatacat -atataatatatatgtaatgt---------------------------------------- ---atatatatgtaatgtatataatatatatgtaatacatatataatatatatgtaatgta -tattatatatgtaatgtatataatatgtatgtaatacatatattatatatgtaatgtata -ttatatatgtattacatatatgtattacatatataacatatatgtattacatatatgtat -tacatatataacatatatgtattacatatatgtaatacacatataatatatatgttatat -atatatatat-------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----atataaaattttttaaaaaattgtttcttgagatagggtctcactctgtcacccagg -ctggagtataatggtttgatcatagttcactgcagccttgaacttctagactcaggtgat -cctcccacctcaacctcct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8684adec8ee8a4e1bad0b9e97757851e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8684adec8ee8a4e1bad0b9e97757851e.msa deleted file mode 100644 index fa594f8d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8684adec8ee8a4e1bad0b9e97757851e.msa +++ /dev/null @@ -1,105 +0,0 @@ ->syndip_1_chr20:20354802-20355545 -tcaggggaggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtca -cactgagaggggaggtggtcagactgtgtcagaggaggtggtcacactgaggggaggtgg -tcacactgtgagaggggaggtggtcagactctgtcagaggaggtggtcacactgtgagag -gggaggtggtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactga -ggggagatggtcacactgcaagaggggaggtgatcacactgagggg-------------- ----------aggtggtcacactgtga-------------------gagggaaggtggtca -cactgtgagagggaaggtggtcacactgtgtgaggggaggtggtcacactgtgaggggag -gtggtcacattgtgagagggaagggggtcactgtgagaggggagaaggtcacactaaggg -gaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgaga -ggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtcacactgaggggagg -tagtgacactatgagcagagatggtcacactgtgaggggaggtggtcacactgaggggag -gtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcacactgagggga -ggtactcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacac--tgagg -ggaggtagtgacactgtgagcagagatggtcacactgtgaggggagggggtcacactgtg -agggggaaggtggtcacactgtgagaggggagaaggtcacactaaggggaggtagtcaca -ctgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagaggaggtggtcac -actgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtcacac -tgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcaca -ctgtgaggggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtggtcac -actgtgaggggaggtggtcacactgaggggaggtagtgacac ->syndip_2_chr20:20354802-20355545 -tcaggggaggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtca -cactgagaggggaggtggtcagactgtgtcagaggaggtggtcacactgaggggaggtgg -tcacactgtgagaggggaggtggtcagactctgtcagaggaggtggtcacactgtgagag -gggaggtggtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactga -ggggagatggtcacactgcaagaggggaggtgatcacactgaggggaggtggtcacactg -tgagagggaaggtggtcacactgtga-------------------gagggaaggtggtca -cactgtgagagggaaggtggtcacactgtgtgaggggaggtggtcacactgtgaggggag -gtggtcacattgtgagagggaagggggtcactgtgagaggggagaaggtcacactaaggg -gaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgaga -ggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtcacactgaggggagg -tagtgacactatgagcagagatggtcacactgtgaggggaggtggtcacactgaggggag -gtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcacactgagggga -ggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacac--tgagg -ggaggtagtgacac---------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------- ->p:HG002_1_chr20:20354802-20355545 -tcaggggaggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtca -cactgagaggggaggtggtcagactgtgtcagaggaggtggtcacactgagg-------- ---------------------------------------ggaggtggtcacactgtgagag -gggaggtggtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactga -ggggagatggtcacactgcaagaggggaggtgatcacactgagggg-------------- ----------aggtggtcacactgtgagaggggaggtgatcacactgagggaaggtggtca -cactgtgagagggaaggtggtcacactgtgtgaggggaggtggtcacactgtgaggggag -gtggtcacattgtgagagggaagggggtcactgtgagaggggagaaggtcacactaaggg -gaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgaga -ggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtcacactgaggggagg -tagtgacactatgagcagagatggtcacactgtgaggggaggtggtcacactgaggggag -gtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcacactgagggga -ggtggtcacactgtgaggggaggtggtcacac--tgaggggaggtggtcacactgtgagg -ggaggtggtcacac---------------------tgtgaggggaggtggtcacactgag -gggaggtag--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------tgacac ->p:HG002_2_chr20:20354802-20355545 -tcaggggaggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtca -cactgagaggggaggtggtcagactgtgtcagaggaggtggtcacactgaggggaggtgg -tcacactgtgagaggggaggtggtcagactctgtcagaggaggtggtcacactgtgagag -gggaggtggtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactga -ggggagatggtcacactgcaagaggggaggtgatcacactgagggg-------------- ----------aggtggtcacactgtga-------------------gagggaaggtggtca -cactgtgagagggaaggtggtcacactgtgtgaggggaggtggtcacactgtgaggggag -gtggtcacattgtgagagggaagggggtcactgtgagaggggagaaggtcacactaaggg -gaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgaga -ggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtcacactgaggggagg -tagtgacactatgagcagagatggtcacactgtgaggggaggtggtcacactgaggggag -gtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcacactgagggga -ggtactcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacac--tgagg -ggaggtagtgacactgtgagcagagatggtcacactgtgaggggagggggtcacactgtg -agggggaaggtggtcacactgtgagaggggagaaggtcacactaaggggaggtagtcaca -ctgtgaggggaggtgatcacactaaggggaggtggtcacactgtgagaggaggtggtcac -actgtgaggggaggtcacactgaggggaggtagtgacactatgagcagagatggtcacac -tgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatggtcaca -ctgtgaggggaggtggtcacactgaggggaggtggtcacactgtgaggggaggtggtcac -actgtgaggggaggtggtcacactgaggggaggtagtgacac ->ref_chr20:20354802-20355545 -tcaggggaggtggtcacactgtgagagaaaaagtaatcacactgtgaggggatgtggtca -cactgagaggggaggtggtcagactgtgtcagaggaggtggtcacactgagg-------- ---------------------------------------ggaggtggtcacactgtgagag -gggaggtggtcacactgaggggaagtggtcacactgtgagaggggaggtggtcacactga -ggggagatggtcacactgcaagaggggaggtgatcacactgagggg-------------- ----------aggtggtcacactgtga-------------------gagggaaggtggtca -cactgtgagagggaaggtggtcacactgtgtgaggggaggtggtcacactgtgaggggag -gtggtcacattgtgagagggaagggggtcactgtgagaggggagaaggtcacactaaggg -gaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgaga -ggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtcacactgaggggagg -tagtgacactatgagcagagatggtcacactgtgaggggaggtggtcacactgaggggag -gtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcacactgagggga -ggtggtcacactgtgaggggaggtggtcacac--tgaggggaggtggtcacactgtgagg -ggaggtggtcacac---------------------tgtgaggggaggtggtcacactgag -gggaggtag--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------tgacac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_86b88a625aacaed9269b0fb36bbeb2b7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_86b88a625aacaed9269b0fb36bbeb2b7.msa deleted file mode 100644 index 1daf60c8..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_86b88a625aacaed9269b0fb36bbeb2b7.msa +++ /dev/null @@ -1,235 +0,0 @@ ->syndip_1_chr20:64125250-64127985 -ggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatctt -gattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactca -aataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgattac -caaagctttatactcaaataccacactgtcttgattaccacagctttatactcaaataac -acaccgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagc -tttatactcaaataccacactgtcttgattaccacagctttatactcaaatactacactg -tcttgattcctatagctttatactcaaataccacactgtcttgattaccacagctttata -ctcaaatactacactgtcttgattactatagctttatactcaaatactacactgtcttga -ttactatagctttatactcaaatactacactgtc-tgattactacagctttatactcaaa -taccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattacca -cagctgtatactcaaatactacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataccacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtcttgattactatagctttatactcaaatactacactgtctgattac -tacagctttatactcaaataccacactatcttgattactacagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacaccgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactacagctttatactcaaataccacaccgt -cttgattaccacagctgtatactcaaatactacaccgtcttgattaccacagctttatac -tcaaatactacaccgtcttgattaccacagctttatactcaaataacacactgtcttgat -tactatagctttatactcaaatactacactgtctgattactacagctttatactcaaata -ccacactgtcttgattaccacagctttatactcaaatactacactgtctgattactacag -ctttatactcaaataccacactgtcttgattaccacagctttatactcaaatactacact -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaataccacactgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctttatactcaaataccacactgtcttgattaccacagctttatacgcaa -ataccacactgtcttgattactatagctttatactcaaataccacactgtcttgattact -acagctttatactcaa--------------------------------------atacca -cactgtcttgattactacagctttatactcaaatactacactgtcttgattaacacagct -ttatactcaaatactacactgtcttgattaccacagctttatactcaaatactacactgt -cttgattactatagctttatactcaaataccacactgtcttgattactatagctttatac -tcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttgat -tactatagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -accacactgtcttgattaccacagctttatactcaaatactacactgtcttgattaccac -agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca -ctgtcttgattactatagctttatactctgttttgaggtcaggtagtgtcagtccctcta -acttcat----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------tt ->syndip_2_chr20:64125250-64127985 -ggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatctt -gattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactca -aataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgattac -caaagctttatactcaaataccacactgtcttgattaccacagctttatactcaaataac -acaccgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagc -tttatactcaaataccacactgtcttgattaccacagctttatactcaaatactacactg -tcttgattcctatagctttatactcaaataccacactgtcttgattaccacagctttata -ctcaaatactacactgtcttgattactatagctttatactcaaatactacactgtcttga -ttactatagctttatactcaaatactacactgtc-tgattactacagctttatactcaaa -taccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattacca -cagctgtatactcaaatactacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataccacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtcttgattactatagctttatactcaaatactacactgtctgattac -tacagctttatactcaaataccacactatcttgattactacagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacaccgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactacagctttatactcaaataccacaccgt -cttgattaccacagctgtatactcaaatactacaccgtcttgattaccacagctttatac -tcaaatactacaccgtcttgattaccacagctttatactcaaataacacactgtcttgat -tactatagctttatactcaaatactacactgtctgattactacagctttatactcaaata -ccacactgtcttgattaccacagctttatactcaaatactacactgtctgattactacag -ctttatactcaaataccacactgtcttgattaccacagctttatactcaaatactacact -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaataccacactgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctttatactcaaataccacactgtcttgattaccacagctttatacgcaa -ataccacactgtcttgattactatagctttatactcaaataccacactgtcttgattact -acagctttatactcaa--------------------------------------atacca -cactgtcttgattactacagctttatactcaaatactacactgtcttgattaacacagct -ttatactcaaatactacactgtcttgattaccacagctttatactcaaatactacactgt -cttgattactatagctttatactcaaataccacactgtcttgattactatagctttatac -tcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttgat -tactatagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -accacactgtcttgattaccacagctttatactcaaataccacactgtcttgattaccac -agctttatactcaaataccacactgtcttgattactatagctttatactcaaataccaca -ctgtcttgattactatagctttatactctgttttgaggtcaggtagtgtcagtccctcta -acttcat----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------tt ->p:HG002_1_chr20:64125250-64127985 -ggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatctt -gattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactca -aataccacaccgtcttgattaccaaagctttatactcaaataccacactgtcttgattac -cacagctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatact -acaccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagc -tttatactcaaatactacactgtcttgattcctatagctttatactcaaataccacactg -tcttgattaccacagctttatactcaaatactacactgtcttgattactatagctttata -ctcaaatactacactgtcttgattactatagctttatactcaaatactacactgtc-tga -ttactacagctttatactcaaataccaccctgtcttgattaccacagctttatactcaaa -taccacaccgtcttgattaccacagctgtatactcaaatac--tactgtcctgattacta -cagctttatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataccacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtcttgattactatagctttatactcaaatactacactgtctgattac -tacagctttatactcaaataccacactatcttgattactacagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacaccgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactacagctttatactcaaataccacaccgt -cttgattaccacagctgtatactcaaatactacaccgtcttgattaccacagctttatac -tcaaatactacaccgtcttgattaccacagctttatactcaaataacacactgtcttgat -tactatagctttatactcaaatactacactgtctgattactacagctttatactcaaata -ccacactgtcttgattaccacagctttatactcaaatactacactgtctgattactacag -ctttatactcaaataccacactgtcttgattaccacagctttatactcaaatactacact -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaataccacactgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctttatactcaaataccacactgtcttgattactatagctttatactcaa -ataccacactgtcttgattaccacagctttatacgcaaataccacactgtcttgattact -atagctttatactcaa--------------------------------------atacca -cactgtcttgattactacagctttatactcaaataccacactgtcttgattactacagct -ttatactcaaatactacactgtcttgattaacacagctttatactcaaatactacactgt -cttgattaccacagctttatactcaaatactacactgtcttgattactatagctttatac -tcaaataccacactgtcttgattactatagctttatactcaaatactacactgtcttgat -taccacagctttatactcaaatactacactgtcttgattactatagctttatactcaaat -accacactgtcttgattaccacagctttatactcaaataccacactgtcttgattaccac -agctttatactcaaataccacactgtcttgattactatagctttatactcaaataccaca -ctgtcttgattactatagctttatactctgttttgaggtcaggtagtgtcagtccctcta -acttcat----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------tt ->p:HG002_2_chr20:64125250-64127985 -ggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatctt -gattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactca -aataccacaccgtcttgattaccaaagctttatactcaaataccacactgtcttgattac -cacagctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatact -acaccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagc -tttatactcaaatactacactgtcttgattcctatagctttatactcaaataccacactg -tcttgattaccacagctttatactcaaatactacactgtcttgattactatagctttata -ctcaaatactacactgtcttgattactatagctttatactcaaatactacactgtc-tga -ttactacagctttatactcaaataccaccctgtcttgattaccacagctttatactcaaa -taccacaccgtcttgattaccacagctgtatactcaaatac--tactgtcctgattacta -cagctttatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataccacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtcttgattactatagctttatactcaaatactacactgtctgattac -tacagctttatactcaaataccacactatcttgattactacagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacaccgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactacagctttatactcaaataccacaccgt -cttgattaccacagctgtatactcaaatactacaccgtcttgattaccacagctttatac -tcaaatactacaccgtcttgattaccacagctttatactcaaataacacactgtcttgat -tactatagctttatactcaaatactacactgtctgattactacagctttatactcaaata -ccacactgtcttgattaccacagctttatactcaaatactacactgtctgattactacag -ctttatactcaaataccacactgtcttgattaccacagctttatactcaaatactacact -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaataccacactgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctttatactcaaataccacactgtcttgattaccacagctttatacgcaa -ataccacactgtcttgattactatagctttatactcaaataccacactgtcttgattact -acagctttatactcaa--------------------------------------atacca -cactgtcttgattactacagctttatactcaaatactacactgtcttgattaacacagct -ttatactcaaatactacactgtcttgattaccacagctttatactcaaatactacactgt -cttgattactatagctttatactcaaataccacactgtcttgattactatagctttatac -tcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttgat -tactatagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -accacactgtcttgattaccacagctttatactcaaatactacactgtcttgattaccac -agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca -ctgtcttgattactatagctttatactctgttttgaggtcaggtagtgtcagtccctcta -acttcat----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------tt ->ref_chr20:64125250-64127985 -ggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatctt -gattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactca -aataccacaccgtcttgattaccaaagctttatactcaaataccacactgtcttgattac -cacagctttatactcaaataacacaccgtcttgattaccacagctttatactcaaatact -acaccgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagc -tttatactcaaatactacactgtcttgattcctatagctttatactcaaataccacactg -tcttgattaccacagctttatactcaaatactacactgtcttgattactatagctttata -ctcaaatactacactgtcttgattactatagctttatactcaaatactacactgtc-tga -ttactacagctttatactcaaataccaccctgtcttgattaccacagctttatactcaaa -taccacaccgtcttgattaccacagctgtatactcaaatac--tactgtcctgattacta -cagctttatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactac -accgtcttgattaccacagctttatactcaaatactacaccgtcttgattaccacagctt -tatactcaaataccacactgtcttgattactatagctttatactcaaatactacactgtc -tgattactacagctttatactcaaataccacactgtcttgattaccacagctttatactc -aaatactacactgtcttgattactatagctttatactcaaatactacactgtctgattac -tacagctttatactcaaataccacactatcttgattactacagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacaccgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactacagctttatactcaaataccacaccgt -cttgattaccacagctgtatactcaaatactacaccgtcttgattaccacagctttatac -tcaaatactacaccgtcttgattaccacagctttatactcaaataacacactgtcttgat -tactatagctttatactcaaatactacactgtctgattactacagctttatactcaaata -ccacactgtcttgattaccacagctttatactcaaatactacactgtctgattactacag -ctttatactcaaataccacactgtcttgattaccacagctttatactcaaatactacact -gtcttgattaccacagctttatactcaaataccacaccgtcttgattaccacagctgtat -actcaaataccacactgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctttatactcaaataccacactgtcttgattactatagctttatactcaa -ataccacactgtcttgattaccacagctttatacgcaaataccacactgtcttgattact -atagctttatactcaaataccacactgtcttgattactacagctttatactcaaatacca -cactgtcttgattactacagctttatactcaaatactacactgtcttgattaacacagct -ttatactcaaatactacactgtcttgattaccacagctttatactcaaatactacactgt -cttgattactatagctttatactcaaataccacactgtcttgattactatagctttatac -tcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttgat -tactatagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -accacactgtcttgattaccacagctttatactcaaataccacactgtcttgattaccac -agctttatactcaaataccacactgtcttgattactatagctttatactcaaataccaca -ctgtcttgattactacagctttatactc-----aaataccacactgtcttgattaacaca -gctttatactcaaatactacactgtcttgattaccacagctttatactcaaatactacac -tgtcttgattactatagctttatactcaaataccacactgtcttgattactatagcttta -tactcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtctt -gattactatagctttgtactcaaataccacactgtcttgattaccacagctttatactca -aataccacactgtcttgattaccacagctttatactcaaataccacactgtcttgattac -tatagctttatactcaaataccacactgtcttgattactacagctttatactcaaatacc -acactgtcttgattactacagctttatactcaaatactacactgtcttgattaacacagc -tttatactcaaatactacactgtcttgattaccacagctttatactcaaatactacactg -tcttgattactatagctttatactcaaataccacactgtcttgattactatagctttata -ctctgttttgaggtcaggtagtgtcagtccctctaacttcattt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8929a4d749057c1b6b994fe58933b454.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8929a4d749057c1b6b994fe58933b454.msa deleted file mode 100644 index 86990116..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8929a4d749057c1b6b994fe58933b454.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:63559305-63559829 -gctgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggt -ggtctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcag -ggtcaggtgggaggg--------------------agtcagggtcaggtgggaggagtca -gggtcagatgggag--------------------tcagtcagagtcaggtgggaggagtc -agggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtc -agggtcagatgggagtcagtcagagtcaggtgggag-gagtcagggtcaggtggga---- --------------ggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtc -agagtcaggtgggaggagtcagggtcaggtgggaggagtcagggt--------------- ----------------------------------------------- ->syndip_2_chr20:63559305-63559829 -gctgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggt -ggtctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcag -ggtcaggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtca -gggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtc -agggtcaggtgggaggagtcagggt----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------- ->p:HG002_1_chr20:63559305-63559829 -gctgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggt -ggtctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcag -ggtcaggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtca -gggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtc -agggtcaggtgggaggagtcagggt----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------- ->p:HG002_2_chr20:63559305-63559829 -gctgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggt -ggtctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcag -ggtcaggtgggaggg--------------------agtcagggtcaggtgggaggagtca -gggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtc -agggtcaggtgggaggagtcagggtcaggt-----------------------cggagtc -agggtcaggtgggag-gagtcagggtcaggtgggagtcagtcagggtcaggtggga---- --------------ggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtc -agagtcaggtgggaggagtcagggtcaggtgggaggagtcagggt--------------- ----------------------------------------------- ->ref_chr20:63559305-63559829 -gctgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggt -ggtctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcag -ggtcaggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtca -gggtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtc -agggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtc -agggtcagatgggagtcagtcagagtcaggtgggag-gagtcagggtcaggtgggaggag -tcagggtcaggtcggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtc -agggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagt -cagagtcaggtgggaggagtcagggtcaggtgggaggagtcagggt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8a7bc612e0bdea73ad6aea0abc428b43.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8a7bc612e0bdea73ad6aea0abc428b43.msa deleted file mode 100644 index 1e6f680f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8a7bc612e0bdea73ad6aea0abc428b43.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:44763796-44764385 -gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt -gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt -tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc -atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc -atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc -atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc -atccatccatccatccatccatccatccatccatttatcc----atccatccatccatcc -acccatccatccatccgtccatccatttatccatccatccatccatccatccatccatcc -atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc -atccacttatccatccacccatccatccatccgtccatccattcatccatccatccatcc -tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt -tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagt ->syndip_2_chr20:44763796-44764385 -gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt -gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt -tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc -atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc -atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc -atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc -atccatccatccatccatccatccatccatccatccatccatttatccatccatccatcc -atccacccatccatccatccgtccatccatttatccatccatccatccatccatccatcc -atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc -atccatttatccatccacccatccatccatccgtccatccattcatccatccatccatcc -tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt -tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagt ->p:HG002_1_chr20:44763796-44764385 -gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt -gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt -tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc -atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc -atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc -atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc -atccatccatccatccatccatccatccatccatccatccatttatccatccatccatcc -atccacccatccatccatccgtccatccatttatccatccatccatccatccatccatcc -atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc -atccatttatccatccacccatccatccatccgtccatccattcatccatccatccatcc -tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt -tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagt ->p:HG002_2_chr20:44763796-44764385 -gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt -gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt -tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc -atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc -atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc -atccatccgtccatccatttatccatccatccatccatccatttatccatccatttatcc -atccatccatccatccatccatccatccatccatttatcc----atccatccatccatcc -acccatccatccatccgtccatccatttatccatccatccatccatccatccatccatcc -atccatttatccatccgtccatttatccatccatccatccacccacccatccatccatcc -atccacttatccatccacccatccatccatccgtccatccattcatccatccatccatcc -tcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacatt -tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagt ->ref_chr20:44763796-44764385 -gactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggtt -gcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacgggt -tccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatcc -atccatccacctatcacttcatccatccatccatttatccatccatccatttatccatcc -atccatccatttatccatccatccatccatttatccatccatccatccatccatccaccc -atccatccgtccatccatttatccatccatccatccatccatttatgcatccatttatcc -atccatccatccatccatccatccatccatccatttatcc-------------------- ------------------------------------------------------------- ------------------------------------------------------------- -atccatccatccatccacccatccatccatccgtccatccattcatccatccatccatcc -tcccacaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatatacatt -tctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaaa -tggggtcagt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8c2dee99b2885a16a73036bed9065e9e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8c2dee99b2885a16a73036bed9065e9e.msa deleted file mode 100644 index 3702693b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8c2dee99b2885a16a73036bed9065e9e.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:45600468-45600847 -aaatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactat -catatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtctt -tgactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctgg -taaaagcagtctctctctctctctctctctctctctctctctctctctatccccccctcc -ctccctccttccctccctccctctctctctctctctccctttctctgtctctccctctct -ctctctctctctccctctctctctctttctccctctctctccctctctctctctctctct -ccctctctctctctttctccctctctctccctctctccccctctctctccctctctccct -ctctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaac -ttgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagc -ccatcataccagctcttcccctggtatattcctaggagtgga ->syndip_2_chr20:45600468-45600847 -aaatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactat -catatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtctt -tgactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctgg -taaaagcagtctctctctctctctctctctctctct--ctctctctctatccccccctcc -ctccctccttccctccctccctctctctctctctctccctttctctgtctctccctctct -ctctctctctctccctctctct-------------------------------------- ---------------------------------------ccctctctccccctctctctcc -ctctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaac -ttgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagc -ccatcataccagctcttcccctggtatattcctaggagtgga ->p:HG002_1_chr20:45600468-45600847 -aaatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactat -catatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtctt -tgactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctgg -taaaagcagtctctctctctctctctctctctctct--ctctctctctatccccccctcc -ctccctccttccctccctccctctctctctctctctccctttctctgtctctccctctct -ctctctctctctccctctctct-------------------------------------- ---------------------------------------ccctctctccccctctctctcc -ctctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaac -ttgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagc -ccatcataccagctcttcccctggtatattcctaggagtgga ->p:HG002_2_chr20:45600468-45600847 -aaatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactat -catatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtctt -tgactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctgg -taaaagcagtctctctctctctctctctctctctctctctctctctctatccccccctcc -ctccctccttccctccctccctctctctctctctctccctttctctgtctctccctctct -ctctctctctctccctctctctctctttctccctctctctccctctctctctctctctct -ccctctctctctctttctccctctctctccctctctccccctctctctccctctctccct -ctctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaac -ttgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagc -ccatcataccagctcttcccctggtatattcctaggagtgga ->ref_chr20:45600468-45600847 -aaatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactat -catatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtctt -tgactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctgg -taaaagcagtctctctctctctctctctctctctct------------------------ ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------------ct -ctatccccccctctccctctctctctacccctgaatctggcctttctaaacaccctcaac -ttgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagc -ccatcataccagctcttcccctggtatattcctaggagtgga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8e86d26235c230b6c03a21914919f32d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8e86d26235c230b6c03a21914919f32d.msa deleted file mode 100644 index ca0778f7..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8e86d26235c230b6c03a21914919f32d.msa +++ /dev/null @@ -1,185 +0,0 @@ ->syndip_1_chr20:18208997-18210827 -gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata -aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta -tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca -cacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagat -gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc -cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc -acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt -ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca -cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta -gacgattccttccacactttccccacacccacacgaacctagacg-attccttccacac- ---ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaa -acctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcca -cacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctaga -cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt -ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac -ctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccaca -ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacacg -aacctaaacgattccttccacaccttctccacacccacacacacctagatgaattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc -acacgaacctagacgattccttccacaccttctccatacccacacgaacctagacaattc -cttccacaccttctcacacccacacaaacctagatgaattccttccacaccttccccaca -cccacacagacctagacgaattccttccacaccttctccacacccacacgaacctagaca -attccttccacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaacctagatgaattccttccacaccttcctcacacccacacgaaccta -gacgattccttccacaccttccccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacgaa -cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac -accttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccaca -cgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac -acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc -ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta -attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagtgca ->syndip_2_chr20:18208997-18210827 -gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata -aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta -tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca -cacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagat -gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc -cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc -acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt -ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca -cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta -gacgattccttccacactttccccacacccacaagaacctagacg-attccttccacac- ---ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaa -acctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcca -cacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctaga -cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt -ccccacacccacacagacctagacgaattccttccacacattctccacacccacacgaac -ctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccaca -ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacacg -aacctaaacgattccttccacaccttctccacacccacacacacctagatgaattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc -acacgaacctagacgattccttccaca------------ccacacgaacctagacaattc -cttccacaccttctcacacccacacaaacctagatgaattccttccacaccttccccaca -cccacacagacctagacgaattccttccacaccttctccacacccacacgaacctagaca -attccttccacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaacctagacgaattccttccacaccttcctcacacccacacgaaccta -gacgattccttccacaccttccccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacgaa -cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac -accttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccaca -cgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac -acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc -ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta -attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagtgca ->p:HG002_1_chr20:18208997-18210827 -gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata -aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta -tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca -cacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagat -gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc -cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc -acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt -ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca -cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta -gacgattccttccacactttccccacacccacaagaacctagacg-attccttccacac- ---ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaa -acctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcca -cacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctaga -cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt -ccccacacccacacagacctagacgaattccttccacacattctccacacccacacgaac -ctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccaca -ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacacg -aacctaaacgattccttccacaccttctccacacccacacacacctagatgaattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc -acacgaacctagacgattccttccaca------------ccacacgaacctagacaattc -cttccacaccttctcacacccacacaaacctagatgaattccttccacaccttccccaca -cccacacagacctagacgaattccttccacaccttctccacacccacacgaacctagaca -attccttccacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaacctagacgaattccttccacaccttcctcacacccacacgaaccta -gacgattccttccacaccttccccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacgaa -cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac -accttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccaca -cgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac -acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc -ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta -attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagttca ->p:HG002_2_chr20:18208997-18210827 -gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata -aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta -tccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccca -cacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctagat -gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc -cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc -acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt -ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca -cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa -ttccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta -gacgattccttccacactttccccacacccacacgaacctagacg-attccttccacac- ---ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacacaa -acctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcca -cacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctaga -cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt -ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac -ctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccaca -ccttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacacg -aacctaaacgattccttccacaccttctccacacccacacacacctagatgaattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc -acacgaacctagacgattccttccacaccttctccatacccacacgaacctagacaattc -cttccacaccttctcacacccacacaaacctagatgaattccttccacaccttccccaca -cccacacagacctagacgaattccttccacaccttctccacacccacacgaacctagaca -attccttccacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaacctagatgaattccttccacaccttcctcacacccacacgaaccta -gacgattccttccacaccttccccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacgaa -cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac -accttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccaca -cgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac -acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc -ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta -attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagtgca ->ref_chr20:18208997-18210827 -gtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaata -aaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgta -tccttccgtagcttctccacacct------------------------------------ ------acacgaacctagacgattccttccacaccttccccacacccacacgaacctagat -gaattccttccacaccttctccacacccacacgaacctagacgattccttccacaccttc -cccacacccattctccacacccacacgaacctagacgattccttccacacctccacaccc -acacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgatt -ccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcca -cacccacacagacctagacgattccttccacacctccacacccacacgaacctagacgaa -ttccttccacaccttgtgcacacccacacgaacctagacgaattccttccacaccttctc -cacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaaccta -gacgattccttccacaccttccccacacccacacagacctagacgaattccttgcacacc -ttctccacacccacacgaacctagacgaattccttccacaccttctccatacccacacga -acctagacaattccttccacaccttct-------------------------------ca -cacccacacaaacctagatgaattccttccacaccttctccacacccacacgaacctaaa -cgattccttccacaccttctccacacccacacacacctagatgaattccttccacacctt -ccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaac -ctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccaca -ccttctcacacccacacaa----------------------------------------- -------------------------------------------acctagatgaattccttc -cacaccttccccacacccacacagacctagacgaattccttccacaccttctccacaccc -acacgaacctagacg--------------------------------------------- ------------------------------------------------------------- --------------------attccttccacaccttccccacacccacacgaacctagaca -attccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttctc -cacacccacacaaacctagacgaattccttccacaccttcctcacacccacacgaaccta -gacgattccttccacaccttccccacacccacacagacctagacgaattccttccacacc -ttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacgaa -cctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttccac -accttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccaca -cgaacctagatgattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacacccac -acaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaattc -ttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatta -attattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccagg -ctggagtgca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_8f863700689b63e4e012e6bd667b5518.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_8f863700689b63e4e012e6bd667b5518.msa deleted file mode 100644 index 4942c214..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_8f863700689b63e4e012e6bd667b5518.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:63535574-63536345 -acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc -ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg -ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaaccac -ctggcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccc -cctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggc -ctcccgcacccccctcacctggcctcccgcccccccctcatctggcctcccgccccctcc -tcacctggcctcccgccccctcctctcctggcctcccgccccccccctcacctggcctcc -cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca -cctggcctcccgccccctcctcacctggcctcccgccccccccctcacctggcctcccgc -cccctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctg -gcctcccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccct -cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc -ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctgg -cctcccgct-ccccccccacctggcctcccaccccctcctcacctggcctcctccccact -tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc -ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtc ->syndip_2_chr20:63535574-63536345 -acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc -ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg -ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------cctggcctcccgccccccccctcacctggcctcc -cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca -cctggcctcccgccccctcctcacctggcctcccg-ccccctcctcacctggcctcccgc -ccccccctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctg -gcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccct -cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc -ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag -cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact -tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc -ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtc ->p:HG002_1_chr20:63535574-63536345 -acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc -ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg -ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------cctggcctcccgccccccccctcacctggcctcc -cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca -cctggcctcccgccccctcctcacctggcctcccg-ccccctcctcacctggcctcccgc -ccccccctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctg -gcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccct -cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc -ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag -cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact -tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc -ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtc ->p:HG002_2_chr20:63535574-63536345 -acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc -ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg -ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaaccac -ctggcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccc -cctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggc -ctcccgcacccccctcacctggcctcccgcccccccctcatctggcctcccgccccctcc -tcacctggcctcccgccccctcctctcctggcctcccgccccccccctcacctggcctcc -cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca -cctggcctcccgccccctcctcacctggcctcccgccccccccctcacctggcctcccgc -cccctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctg -gcctcccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccct -cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc -ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctgg -cctcccgct-ccccccccacctggcctcccaccccctcctcacctggcctcctccccact -tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc -ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtc ->ref_chr20:63535574-63536345 -acttccaggtggagcttgcagaagctccaggtgacctgcgccctttgtgtgtctgactcc -ctcaggtcactggaacacaaaccccacacagaagaccacggcccagcatggagcccctgg -ggtccaccccctccacttccgcacacctggaagcactgccccacctgcccctccaacca- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------cctggcctcccgccccccccctcacctggcctcc -cgccccctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctca -cctggcctcccgccccctcctcacctggcctcccg-ccccctcctcacctggcctcccgc -ccccccctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctg -gcctcccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccct -cctctcctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctc -ccgccccccccacctggcctcccgccccccctcacctggcctccagccccccccacctag -cctcccgctcccccccccacctggcctcccaccccctcctcacctggcctcctccccact -tctcacctgggcgagttctcaggactcagggtctttgcacctgggagctgaccagcctcc -ggccagaccccacccctgcacccctgctcactaacgaggtcgtgggtctgcgcgtgaccc -tgctaacgaggtcgtgggtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_92be9763c7114fd6ce736a7008114ad0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_92be9763c7114fd6ce736a7008114ad0.msa deleted file mode 100644 index 706d7b25..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_92be9763c7114fd6ce736a7008114ad0.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:14861944-14862754 -agtgaaataggacattggaggttttatatataaatatatatatatatatttatatatata -tttatatatatatatttatatatatttatatatatttatatatatatttatatatatat- --ttatatatatatttatatatatatttatatatatatttatatatatatttatatatata -tttatatatatttatatatatttatatatatttttatatatttttatatatataaatata -taaaaatatatataaatatataaaaatatataaaaatatataaatatatataaatatata -aatatatataaatatatataaatatatatttatatataaatatatataaatatatattta -tacataaatatatataaatatatatttatacataaatatataaatatatataatatatat -aaatatatattatacatatatatataaatatatattatacataaatatataaatatatat -aaatatatataaatatatatttatacataaatatataaatatatatataaatatatataa -atatatataaatatatatataaatatatatataaatatatataaatatatatataaatat -atatataaatatatataaatatatataaatatatatataaatatatataaatatatataa -atatatatttatatattaatatataaatatatataa-atatatatttatatatta----- ---atatataaatatat-----------atatattaatatatataaatatatataaatata -tatttatatattaatatatatatattaatatatatatatttatatattaatatatatatt -tatatattaatatatataaatatattactatgtatatttatatatatttatataaatata -tataaatatatgtaaatatatatataaaaatatatattaatatataaaaatatatatata -aatata---tataaatatatatataaatatatataaatatatatatataaatatatataa -ataaatatataaatatatataaatat--atatataaatatatataaatatatataaatat -atataaaaatatatataaatatatatataaatatatataaatatatatataaatatatat -ataaatatatatataaatatatataa--atatatatataaatatatataaatatatatat -aattatatataaatatatataaatatatataaatatatatataaatatatataaatatat -ataaatatatataaatatatatataaatatatataaatatatatatataaatatatataa -atatatatataaatatatataaatatatatataaatataaatatatataaatata----t -aaaaatatatatataaatataaatatatataaatatatatgtataaatatatatataa-- ---------atataaatatatatatataaatatatatataaatatatatatataaatatat -atataaatatatataaatatatatataaatatatataaatatatatatatatattttttt -ttaatagagaggatgaagaccaaagcagtgag ->syndip_2_chr20:14861944-14862754 -agtgaaataggacattggaggtttt----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------atatataaatatatat -atatatatttatatatatatttatatatatatatttatatatatttatatatatttatat -atatatttatatatatatttatatatatttatatatttatatatatttatatatattttt -atatatataaatatataaaaatatataaatatatat----aaatatataaatatatataa -atatatatttatacataaatatataaatatatataatatatataaatatatattatacat -atatatataaatatatattatacataaatatataaatatatataaatatatataaatata -tatttatacataaatatataaat----atatatatatataaatatatataaatatatatt -tatatattaatatatataaatatattactatgtatatttatatatatttatataaatata -tataaatatatgtaaatatatatataaaaatatatattaatatataaaaatatatatata -aatata-------------tatataaatatatataaataaatatatataaatatatatat -aaatatatataaatatatataaatat--atatataaatatatataaatatatataaatat -atatataaatatatatataaatatatataaatatatataaataaatatataaatatatat -ataaatatatataaatatatatataaatatatataaatatatatatataaatatatataa -atatatatataaatatatataaatat------atatataaatatatataaatatatatat -ataaatatatataaatatatatataaatatatataaatatat--------atataaatat -aaatatatataaatatataaaaatatatatataaatataaatatatataaatatatatgt -ataaatatatatataaatataaatatatataaatatatatatataaatatatatataa-- ---------atatatataaatatatataaaaatatatataa--atatatatataaatatat -atataaatatatataaatatatatataaatatatataaatatatatatatatattttttt -ttaatagagaggatgaagaccaaagcagtgag ->p:HG002_1_chr20:14861944-14862754 -agtgaaataggacattggaggtttt----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------atatataaatatatat -atatatatttatatatatatttatatatatatatttatatatatttatatatatttatat -atatatttatatatatatttatatatatttatatatttatatatatttatatatattttt -atatatataaatatataaaaatatataaatatatat----aaatatataaatatatataa -atatatatttatacataaatatataaatatatataatatatataaatatatattatacat -atatatataaatatatattatacataaatatataaatatatataaatatatataaatata -tatttatacataaatatataaat----atatatatatataaatatatataaatatatatt -tatatattaatatatataaatatattactatgtatatttatatatatttatataaatata -tataaatatatgtaaatatatatataaaaatatatattaatatataaaaatatatatata -aatata-------------tataaatatatatataaataaatatatataaatatatatat -aaatatatataaatatatataaatat--atatataaatatatataaatatatataaatat -atatataaatatatatataaatatatataaatatatataaataaatatataaatatatat -ataaatatatataaatatatatataa--atatataaatatatatatataaatatatataa -atatatatataaatatatataaatat------atatataaatatatataaatatatatat -ataaatatatataaatatatatataaatatatataaatatat--------atataaatat -aaatatatataaatatataaaaatatatatataaatataaatatatataaatatatatgt -ataaatatatatataaatataaatatatataaatatatatatataaatatatatataa-- ---------atatatataaatatatataaaaatatatataa--atatatatataaatatat -atataaatatatataaatatatatataaatatatataaatatatatatatatattttttt -ttaatagagaggatgaagaccaaagcagtgag ->p:HG002_2_chr20:14861944-14862754 -agtgaaataggacattggaggttttatatataaatatatatatatatatttatatatata -tttatatatatatatttatatatatttatatatatttatatatatatttatatatatata -aatatatataaatatataaatatatataaatatatatttatacataaatatataaatata -tttatatatatttatatatatttatatatatttttatatatttttatatatataaatata -taaaaatatatataaatatataaaaatatataaaaatatataaatatatataaatatata -aatatatataaatatatataaatatatatttatatataaatatatataaatatatattta -tacataaatatatataaatatatatttatacataaatatataaatatatataatatatat -aaatatatattatacataaatatataaatatatattatacataaatatataaatatatat -aaatatatataaatatatatttatacataaatatataaatatatatataaatatatataa -atatatataaatatatatataaatatatatataaatatatataaatatatatataaatat -atatataaatatatataaatatatataaatatatatataaatatatataaatatatataa -atatatatttatatattaatatataaatatatataa-atatatatttatatatta----- ---atatataaatatat-----------atatattaatatatataaatatatataaatata -tatttatatattaatatatatatattaatatatatatatttatatattaatatatatatt -tatatattaatatatataaatatattactatgtatatttatatatatttatataaatata -tataaatatatgtaaatatatatataaaaatatatattaatatataaa---atatatata -aatatatattatacataaatatataaatatatataaatatatataaatatatatttatac -ataaatatataaatatatatatatataaatatatataaatatatatttatatattaatat -atataaatatattactatgtatatttatatatatttatataaatatatataaatatatgt -aaatatatatataaaaatatatatta--atatataaaaatatatatataaatatatataa -atatatatataaatatatataaatat------atatatataaatatatataaatatatat -ataaatatatataaatatatatataaatatatataaatatatatatataaatatatataa -atatatatataaatatatataaatatatatataaatataaatatatataaatata----t -aaaaatatatatataaatataaatatatataaatatatatgtataaatatatatataa-- ---------atataaatatatatatataaatatatatataaatatatatatataaatatat -atataaatatatataaatatatatataaatatatataaatatatatatatatattttttt -ttaatagagaggatgaagaccaaagcagtgag ->ref_chr20:14861944-14862754 -agtgaaataggacattggaggttt------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------tatatataaatata -tatatatatatt--tatatatatatttatatatatatatttatatatatttatatatatt -tatata----------------------tatatttatatatatataaatatatataaata -tataaatatatataaatatatatttatacataaatatataaatatata---atatatata -aatatatattatacataaatatataaatatatataaatatatataaatatatatttatac -ataaatatataaatatatatatatataaatatatataaatatatatttatatattaatat -atataaatatattactatgtatatttatatatatttatataaatatatataaatatatgt -aaatatatatataaaaatatatatta--atatataaaaatatatatataaatatatataa -atatatatataaatatatataaatat------atatatataaatatatataaatatatat -ataaatatatataaatatatatataaatatatataaatatatatatataaatatatataa -atatatatataaatatatataaatatatatataaatataaatatatataaatata----t -aaaaatatatatataaatataaatatatataaatatatatgtataaatatatatataaat -ataaatatatataaatatatatatataaatatatatataaatatatatatataaatatat -atataaatatatataaatatatatataaatatatataaatatatatatatatattttttt -ttaatagagaggatgaagaccaaagcagtgag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9332ea6154bb7492be1f52b51104342c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9332ea6154bb7492be1f52b51104342c.msa deleted file mode 100644 index 3299c789..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9332ea6154bb7492be1f52b51104342c.msa +++ /dev/null @@ -1,50 +0,0 @@ ->syndip_1_chr20:50775536-50775942 -ggtattctgctttctcattctgtctctccaaagatttccatatatatatatatatatata -tatatatatatatatatatataaatataaatatattctatatattcatatatatatattc -tatatattcatatatataaatatattctatatattcatatataaatatattccatatata -taaatatattccatatatt---tatatataaatatatatcatatatttatatataaatat -atatcatatatttatatataaatatatatcatatatttatatat-aatatatatcatata -tttatatataaatatatatcatatatttatatataaatatatatcatatatttatatata -atatatatcatata-ttatatataaatatatatcatatatttatatataaatatatatca -tatattaatatatatcatatatttatatattaatatatatcatatatttatatattaata -tatat ->syndip_2_chr20:50775536-50775942 -ggtattctgctttctcattctgtctctccaaagatttccatatatatatatatatatata -tatatatatatatatatatataaatataaatatattctatatattcatatatatatattc -tatatattcatatatataaatatattctatatattcatatatataaatatattctatata -ttcatata-taaatatattccatatatataaatatattccatatatttatatataaatat -atatcatatatttatatataaatatatatcatatatttatatataaatatatatcatata -tttatatat-aatatatatcatatatttatatataaatatatatcatatatttatatata -atatatatcatata-ttatatataaatatatatcatatatttatatataaatatatatca -tatattaatatatatcatatatttatatattaatatatatcatatatttatatattaata -tatat ->p:HG002_1_chr20:50775536-50775942 -ggtattctgctttctcattctgtctctccaaagatttccatatatatatatatatatata -tatatatatatatatatatataaatataaatatattctatatattcatatatatatattc -tatatattcatatatataaatatattctatatattcatatataaatatatattctatata -ttcatata-taaatatattccatatatataaatatattccatatatttatatataaatat -atatcatatccatatatataaatatattccatatatttatatataaatatatatcatata -tttatatataaatatatatcatatatttatatataaatatatatcatatatttatatata -atatatatcatatatttatatataaatatatatcatatatttatatataaatatatatca -tatattaatatatatcatatatttatatattaatatatatcatatatttatatattaata -tatat ->p:HG002_2_chr20:50775536-50775942 -ggtattctgctttctcattctgtctctccaaagatttccatatatatatatatatatata -tatatatatatatatatatataaatataaatatattctatatattcatatatatatattc -tatatattcatatatataaatatattctatatattcatatataaatatattccatatata -taaatatattccatatatt---tatatataaatatatatcatatatttatatataaatat -atatcatatatttatatataaatatatatcatatatttatatat-aatatatatcatata -tttatatataaatatatatcatatatttatatataaatatatatcatatatttatatata -atatatatcatata-ttatatataaatatatatcatatatttatatataaatatatatca -tatattaatatatatcatatatttatatattaatatatatcatatatttatatattaata -tatat ->ref_chr20:50775536-50775942 -ggtattctgctttctcattctgtctctccaaagatttccatatatatatatatatatata -tatatatatatatatatatataaatataaatatattctatatattcatatatatatattc -tatatattcatatatataaatatattctatatattcatatataaatatattccatatata -taaatatattccatatatt---tatatataaatatatatcatatatttatatataaatat -atatcatatatttatatataaatatatatcatatatttatatat-aatatatatcatata -tttatatataaatatatatcatatatttatatataaatatatatcatatattaatatata -tcatatat-------ttatatattaatatatatcatatatttatatattaatatatat-- ------------------------------------------------------------- ------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_94d3450a4e5e36376aa498c7604db789.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_94d3450a4e5e36376aa498c7604db789.msa deleted file mode 100644 index 745d8bbc..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_94d3450a4e5e36376aa498c7604db789.msa +++ /dev/null @@ -1,170 +0,0 @@ ->syndip_1_chr20:8661810-8662758 -agccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggca -agaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactc -ctcttaaaagtgtatatatatataattatataattatttattatataattatatataatt -atataattatttattatataattatatataattatataattatttattatataattatat -ataa-tatacaattatttattatataattatatataattatatatttattatatttat-- ----tatacagttatataataaataattatataattatatataattatata---------t -atataattatatataattatata-----taattatataattatatataattg-------- ------------------------tatataattatttattatataattatat--------- ---attatttattatataattatata----------------attatat------------ -------attatttattatata--------------------------------------- ----------------------ttatataattatataattatatattatttattatata-- ----atatataattatatat-------tatttattatataattatatattatttatta--- -------tatatattatttattatata----------------------attatatattat -gtattatataattatataattatatattatgtattatataat----------------ta -tatattatgtattatataattatataattatatattatgtattatataattatatattat -ttattatataattatataattatatattatttattatataattatataattatatattat -ttattatataat---------------------tatataattatatattatttattatat -aattatataattatat-attattt--------attatataattatatattatttattata -taattatatattatttattacataaatatatattatttattacataagtatatatcactt -attatataattgcatataattatttattatataattgcatataa----ttattatataat -tgtatatagttatttattatataattgtatatagttatttattatataattctatataat -tatttattatctaattctatattaaatataattatttattatc----------------- ----------------taattctatattatatataattatttattatataattctatatta -tatataattattatataattctatatataattatttattatataattctatacataagta -tttattatataattatgtatataattatttattatataattatgtataatatgtaattat -ttattatataattatgtataatatgtaattatttattatataattatgtataatatataa -ttatttattatataattatgtataatatataattatttattatataattatgtgttatgt -ataa----ttattatataattatgtataatatatatataattttttattatataattatg -tataatatataattttttataattatgtgtaatatataattatttatcatataattacaa -tatatattattaacataatatctaaatatattaataatctaatatctataattaatataa -tatataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaa -atgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagc -aaaggcccacacc ->syndip_2_chr20:8661810-8662758 -agccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggca -agaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactc -ctcttaaaagtgtatatatatataattatataattatttattatataatgatatataatt -atataattatttattatataatgatatataattatataattatttattatataattatat -ataattatataattatttattatataattatatataattatataattatttattatataa -ttatatataattatataattatttattatataattatatataattatataattatttatt -atataattatatataattatataattatttattatataattatatataattatataatta -tttattatataattatatataattatataattatttattatataattatatataattata -taattatttattatataattatatataatatacaattatttattatataattatatataa -tatacaattatttattatataattatatataattatatatttattatatttattatacag -ttatataataaatatataattatatataaatatataattatatataattatatatatata -attatatgtaattatatataattatataattattatataattgtatataatatataatta -tataattatatattatttattatataatatataattatataattatatattatttattat -ataatatataattatataattatatattatttattatataattatatattatttattata -tatattatttattatataattatataattatatattatttattatataattatatattat -ttattatataa-tatataattatatattatttattatataa-tatataattatatattat -ttattatataattatatattatgtattatataatatataattatatattatgtattatat -aattatataattatat-attatttattatataattatataattatatattatttattaca -taattatatattatttattacataagtatatattatttattacataagtatatatcactt -attatataattgtatataattatttattatataattgcatataattatttattatataat -tgtatatagttatttattatataattctatatagttatttattatataattctatataat -tatttattatctaattctatattatatataattatttattatctaattctatattatata -taattatttattatataattctatattatatataattatttattatataattctatatta -tatataattattatataattctatatataattatttattatataattctatacataagta -tttattatataattatgtatataattatttattatataattatgtataatatgtaattat -ttattatataattatgtataatatataattgtttattatataattatgtataatatataa -ttatttattatataattatgtataatatataattatttattatataattatgtgttatgt -ataattatttattatataattatgtataatatatatataattttttattatataattatg -tataatatataattttttataattatgtgtaatatataattatttatcatataattacaa -tatatattattaacataatatctaaatatattaataatctaatatctataattaatataa -tatataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaa -atgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagc -aaaggcccacacc ->p:HG002_1_chr20:8661810-8662758 -agccaacctacgttaagtaattcataacttcagtattcaataaatcttcagtgaaaggca -agaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactc -ctcttaaaagtgtatatatatataattatataattatttattatataatgatatataatt -atataattatttattatataatgatatataattatataattatttattatataattatat -ataattatataattatttattatataattatatataattatataattatttattatataa -ttatatataattatataattatttattatataattatatataattatataattatttatt -atataattatatataattatataattatttattatataattatatataattatataatta -tttattatataattatatataattatataattatttattatataattatatataattata -taattatttattatataattatatataatatacaattatttattatataattatatataa -tatacaattatttattatataattatatataattatatatttattatatttattatacag -ttatataataaatatataattatatataaatatataattatatataattatatatatata -attatatgtaattatatataattatataattattatataattgtatataatatataatta -tataattatatattatttattatataatatataattatataattatatattatttattat -ataatatataattatataattatatattatttattatataattatatattatttattata -tatattatttattatataattatataattatatattatttattatataattatatattat -ttattatataa-tatataattatatattatttattatataa-tatataattatatattat -ttattatataattatatattatgtattatataatatataattatatattatgtattatat -aattatataattatat-attatttattatataattatataattatatattatttattaca -taattatatattatttattacataagtatatattatttattacataagtatatatcactt -attatataattgtatataattatttattatataattgcatataattatttattatataat -tgtatatagttatttattatataattctatatagttatttattatataattctatataat -tatttattatctaattctatattatatataattatttattatctaattctatattatata -taattatttattatataattctatattatatataattatttattatataattctatatta -tatataattattatataattctatatataattatttattatataattctatacataagta -tttattatataattatgtatataattatttattatataattatgtataatatgtaattat -ttattatataattatgtataatatataattgtttattatataattatgtataatatataa -ttatttattatataattatgtataatatataattatttattatataattatgtgttatgt -ataattatttattatataattatgtataatatatatataattttttattatataattatg -tataatatataattttttataattatgtgtaatatataattatttatcatataattacaa -tatatattattaacataatatctaaatatattaataatctaatatctataattaatataa -tatataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaa -atgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagc -aaaggcccacacc ->p:HG002_2_chr20:8661810-8662758 -agccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggca -agaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactc -ctcttaaaagtgtatatatatataattatataattatttattatataattatatataatt -atataattatttattatataattatatataattatataattatttattatataattatat -ataa-tatacaattatttattatataattatatataattatatatttattatatttat-- ----tatacagttatataataaataattatataattatatataattatata---------t -atataattatatataattatata-----taattatataattatatataattg-------- ------------------------tatataattatttattatataattatat--------- ---attatttattatataattatata----------------attatat------------ -------attatttattatata--------------------------------------- ----------------------ttatataattatataattatatattatttattatata-- ----atatataattatatat-------tatttattatataattatatattatttatta--- -------tatatattatttattatata----------------------attatatattat -gtattatataattatataattatatattatgtattatataat----------------ta -tatattatgtattatataattatataattatatattatgtattatataattatatattat -ttattatataattatataattatatattatttattatataattatataattatatattat -ttattatataat---------------------tatataattatatattatttattatat -aattatataattatat-attattt--------attatataattatatattatttattata -taattatatattatttattacataaatatatattatttattacataagtatatatcactt -attatataattgcatataattatttattatataattgcatataa----ttattatataat -tgtatatagttatttattatataattgtatatagttatttattatataattctatataat -tatttattatctaattctatattaaatataattatttattatc----------------- ----------------taattctatattatatataattatttattatataattctatatta -tatataattattatataattctatatataattatttattatataattctatacataagta -tttattatataattatgtatataattatttattatataattatgtataatatgtaattat -ttattatataattatgtataatatgtaattatttattatataattatgtataatatataa -ttatttattatataattatgtataatatataattatttattatataattatgtgttatgt -ataa----ttattatataattatgtataatatatatataattttttattatataattatg -tataatatataattttttataattatgtgtaatatataattatttatcatataattacaa -tatatattattaacataatatctaaatatattaataatctaatatctataattaatataa -tatataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaa -atgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagc -aaaggcccacacc ->ref_chr20:8661810-8662758 -agccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggca -agaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactc -ctcttaaaag-------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------tgtat -atatatataattatataattattt--------attatataattatatataattatata-- ----------attatttattatataattatatataatatac------------aattattt -attatataattatatataattatat--------atttattatat----ttattatacagt ---tatataataaataattatataattatatataattatat------------------at -tatttattatctaattctatattaaatataattatttattatc----------------- ----------------taattctatattatatataattatttattatataattctatatta -tatataattattatataattctatatataattatttattatataattctatacataagta -tttattatataattatgtatataattatttattatataattatgtataatatgtaattat -ttattatataattatgtataatatgtaattatttattatataattatgtataatatataa -ttatttattatataattatgtataatatataattatttattatataattatgtgttatgt -ataa----ttattatataattatgtataatatatatataattttttattatataattatg -tataatatataattttttataattatgtgtaatatataattatttatcatataattacaa -tatatattattaacataatatctaaatatattaataatctaatatctataattaatataa -tatataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaa -atgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagc -aaaggcccacacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_96144f7364730e7be7deffcbdb716db1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_96144f7364730e7be7deffcbdb716db1.msa deleted file mode 100644 index bc5a698f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_96144f7364730e7be7deffcbdb716db1.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:5039848-5040600 -gagacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatg -tgagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacag -gtattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagca -tttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtacttt -gggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaa -agtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgtt -gtcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagctt -cagttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc -aaaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctt -agcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcc -tgggcaacatagggagaacttgtctctattt----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcc -tcaaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggc -aacccggattagcctttt ->syndip_2_chr20:5039848-5040600 -gagacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatg -tgagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacag -gtattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagca -tttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtacttt -gggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaa -agtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgtt -gtcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagctt -cagttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc --aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctt -agcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcc -tgggcaacatagggagaacttgtctctattt----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcc -tcaaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggc -aacccggattagcctttt ->p:HG002_1_chr20:5039848-5040600 -gagacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatg -tgagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacag -gtattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagca -tttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtacttt -gggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaa -agtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgtt -gtcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagctt -cagttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc --aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctt -agcactctttgggaggctgagactggaggatcttttgagcccaggggtttgagaccagcc -tgggcaacatagggagaacttgtctctatttaaaaaaaaaggccgggcgcggtggctcac -gcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtcaggagatcga -gaccatcctggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccgg -gcgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagt -gagccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgt -ctcaaaaaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcc -tcaaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggc -aacccggattagcctttt ->p:HG002_2_chr20:5039848-5040600 -gagacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatg -tgagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacag -gtattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagca -tttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtacttt -gggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaa -agtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgtt -gtcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagctt -cagttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc -aaaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctt -agcactctttgggaggctgagactggaggatcttttgagcccaggggtttgagaccagcc -tgggcaacatagggagaacttgtctctattttaaaaaaaaggccgggcgcggtggctcac -gcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtcaggagatcga -gaccatcctggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccgg -gcgcggtggcgggcgcctaggcaggagaatggcgtgaacccgggaagcggagcttgcagt -gagccgagattgcgccactgcagtccgcagtccgacctgggcgacagagagagactccgt -ctc---aaaaaaaaaaaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcc -tcaaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggc -aacccggattagcctttt ->ref_chr20:5039848-5040600 -gagacacagtgtccaggattgcattatgtggccaccccagatgaaggggagatgagaatg -tgagtgttccgttttctaatatgtataatacaggtaggctgggcagaaagagttagacag -gtattgggttagccagcctacagtgtctaacacaccaacaaaatcaagcattggagagca -tttggatatggaagagtgctgagaaggtgtggtggctcatgcctataatcctagtacttt -gggaggctgaggcaggaggatcacttaagtccaggagtttgagagcagcctgggcaacaa -agtgagaccttgtctctacaaaaaataaacaaaattagctggtggtggcacctgcctgtt -gtcccagctactcagggggctgaggtgggaggatggcttgagcctgggagattgaagctt -cagttagccatgatcatgccactgcgctccagcctgggtgacagagagagatcctgcctc --aaaaaaaaaataaaaataaaaaagaggggccgggtgtggtggctcaggcctgtaatctt -agcactctttgggaggctgagactggaggatcctttgagcccaggggtttgagaccagcc -tgggcaacatagggagaacttgtctctattt----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------aaaaaaaaaaatgctcatacgtggttggcaggagtgtaaatagcc -tcaaccaatttggaaagcaatttgccaatactagttaatataacgatctagatagtgggc -aacccggattagcctttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9aaaa5726b19af71cbe6bbc7fffce373.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9aaaa5726b19af71cbe6bbc7fffce373.msa deleted file mode 100644 index d0fbe6c4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9aaaa5726b19af71cbe6bbc7fffce373.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:63535641-63536112 -cactggaacacaaaccccacacagaagaccacggcccagcatggagcccctggggtccac -cccctccacttccgcacacctggaagcactgccccacctgcccctccaaccacctggcct -cccg-cccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcct -cacctggcctcccg-cccccccctcacctggcctcccaccccgtcctcacctggcctccc -gcacccccctcacctggcctcccgcccccccctcatctggcctcccgccccctcctcacc -tggcctcccgccccctcctctcctggcctcccgccccccccctcacctggcctcccgccc -cctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctcacctgg -cctcccgccccctcctcacctggcctcccgccccccccctcacctggcctcccgccccct -cctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacctggcctc -ccgcacccccctcacctggcctcccgcccccccctcacctggcctcccgccccctcctct -cctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctcccgcc -ccccccacctggcctcccgccc ->syndip_2_chr20:63535641-63536112 -cactggaacacaaaccccacacagaagaccacggcccagcatggagcccctggggtccac -cccctccacttccgcacacctggaagcactgccccacctgcccctccaaccacctggcct -cccgccccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcct -cacctggcctcccgccccccccctcacctggcctcccgccccctcctcacctggcctccc -gccccctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacc -tggcctcccgcacccccctcacctggcctcccg-cccccccctcacctggcctcccgccc -cctcctcacctggcctcccgccccctcctctcctggcctcccg-ccccctcctctcctgg -cctcccgtcccctcctctcctggtctcccgccccccc---cacctggcctcccgccc--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------- ->p:HG002_1_chr20:63535641-63536112 -cactggaacacaaaccccacacagaagaccacggcccagcatggagcccctggggtccac -cccctccacttccgcacacctggaagcactgccccacctgcccctccaaccacctggcct -cccgccccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcct -cacctggcctcccgccccccccctcacctggcctcccgccccctcctcacctggcctccc -gccccctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacc -tggcctcccgcacccccctcacctggcctcccg-cccccccctcacctggcctcccgccc -cctcctcacctggcctcccgccccctcctctcctggcctcccg-ccccctcctctcctgg -cctcccgtcccctcctctcctggtctcccgccccccc---cacctggcctcccgccc--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------- ->p:HG002_2_chr20:63535641-63536112 -cactggaacacaaaccccacacagaagaccacggcccagcatggagcccctggggtccac -cccctccacttccgcacacctggaagcactgccccacctgcccctccaaccacctggcct -cccg-cccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcct -cacctggcctcccg-cccccccctcacctggcctcccaccccgtcctcacctggcctccc -gcacccccctcacctggcctcccgcccccccctcatctggcctcccgccccctcctcacc -tggcctcccgccccctcctctcctggcctcccgccccccccctcacctggcctcccgccc -cctcctcacctggcctcccgccccctcctcacctggcctcccgccccccccctcacctgg -cctcccgccccctcctcacctggcctcccgccccctc-ctcacctggcctcccgcccccc -cctcacctggcctcccaccccgtcctcacctggcctcccgcacccccctcacctggcctc -ccgcccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcctct -cctggcctcccgccccctcctctcctggcctcccgtcccctcctctcctggtctcccgcc -ccccccacctggcctcccgccc ->ref_chr20:63535641-63536112 -cactggaacacaaaccccacacagaagaccacggcccagcatggagcccctggggtccac -cccctccacttccgcacacctggaagcactgccccacctgcccctccaaccacctggcct -cccgccccccccctcacctggcctcccgccccctcctcacctggcctcccgccccctcct -cacctggcctcccgccccccccctcacctggcctcccgccccctcctcacctggcctccc -gccccctcctcacctggcctcccgcccccccctcacctggcctcccaccccgtcctcacc -tggcctcccgcacccccctcacctggcctcccg-cccccccctcacctggcctcccgccc -cctcctcacctggcctcccgccccctcctctcctggcctcccg-ccccctcctctcctgg -cctcccgtcccctcctctcctggtctcccgccccccc---cacctggcctcccgccc--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9b9b387681fd363ece224e3813679abe.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9b9b387681fd363ece224e3813679abe.msa deleted file mode 100644 index 80617d12..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9b9b387681fd363ece224e3813679abe.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:61561820-61562603 -acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc -ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt -ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg -accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc -ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg -acttccgtgtggagaggtggaccccagggctcccggagagagagagggacctccctgaga -gagagagggacctccctgtggagaggtggaccccagggctcccggagagagagagggacc -tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga -ggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtggaccccag -ggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccggaga -gagggacctccgtgtggagagctggaccccagggctcccggagagagagagggacctccg -tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagagagggaccttcgtgtggagaggtggaccccaggact -cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag -gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagcc ->syndip_2_chr20:61561820-61562603 -acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc -ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt -ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg -accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc -ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg -acctccg----------------------------------------------------- -----------------tgtggagaggtggaccccagggctcccggagagagagagggacc -tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga -ggtggaccccagggctcccgga-------------------------------------- ---------------------------------------------------------gaga -gagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctg -tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact -cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag -gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagcc ->p:HG002_1_chr20:61561820-61562603 -acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc -ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt -ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg -accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc -ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg -acctccg----------------------------------------------------- -----------------tgtggagaggtggaccccagggctcccggagagagagagggacc -tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga -ggtggaccccagggctcccgga-------------------------------------- ---------------------------------------------------------gaga -gagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctg -tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact -cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag -gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagcc ->p:HG002_2_chr20:61561820-61562603 -acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc -ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt -ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg -accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc -ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg -acttccgtgtggagaggtggaccccagggctcccggagagagagagggacctccctgaga -gagagagggacctccctgtggagaggtggaccccagggctcccggagagagagagggacc -tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga -ggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtggaccccag -ggctcccggagagagagagggacctccgtgtggagaggtggaccccagggctcccggaga -gagggacctccgtgtggagagctggaccccagggctcccggagagagagagggacctccg -tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagagagggaccttcgtgtggagaggtggaccccaggact -cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag -gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcatccctgcaggatctgagcacagaacggcctgcttcagcc ->ref_chr20:61561820-61562603 -acaacccacaaaggtttatagctcctttcctgtgctgaagagctggcccttctctgggcc -ccagtggctgcatgcgccatgtttctgggcagtgaccatatgatggcagtaatgctgtgt -ctggaaatcctgaccccagggctcccagagagagagagggaccttcgtgtggagaggtgg -accccagggctcccggagagagagaggggccttcgtgtggagaggtggaccccagggctc -ccggagagagagaggggcctccgtgtggagaggtggaccccagggctcccggagagaggg -acctccg----------------------------------------------------- -----------------tgtggagaggtggaccccagggctcccggagagagagagggacc -tccctgtggagaggtggaccccagggctcccagagagagagagggaccttcgtgtggaga -ggtggaccccagggctcccgga-------------------------------------- ---------------------------------------------------------gaga -gagggacctccgtgtggagaggtggaccccagggctcccggagagagagagggacctctg -tgtggagaggtggaccccagggctcccggagagagagagggacctccgtgtggagaggtg -gaccccagggctcccggagagagagggggaccttcgtgtggagaggtggaccccaggact -cccggagagagagaggggcctccgtgtgcagaggtggtttgtcgcttctttcatcttcag -gacagtcattgcctgggaaactggggggattggtccgaacccaccttgtacaccccagac -ttggtgcgtccctgcaggatctgagcacagaacggcctgcttcagcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9cd197dc9e9fcfccd187bb2ad2196c04.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9cd197dc9e9fcfccd187bb2ad2196c04.msa deleted file mode 100644 index b47b4a62..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9cd197dc9e9fcfccd187bb2ad2196c04.msa +++ /dev/null @@ -1,185 +0,0 @@ ->syndip_1_chr20:18208996-18210828 -ggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaat -aaaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgt -atccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccc -acacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctaga -tgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacctt -ccccacacccattctccacacccacacgaacctagacgattccttccacacctccacacc -cacacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgat -tccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcc -acacccacacagacctagacgattccttccacacctccacacccacacgaacctagacga -attccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttct -ccacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacct -agacgattccttccacactttccccacacccacacgaacctagacg-attccttccacac ----ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacaca -aacctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcc -acacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctag -acgattccttccacaccttctccacacccacacacacctagatgaattccttccacacct -tccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaa -cctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccac -accttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacac -gaacctaaacgattccttccacaccttctccacacccacacacacctagatgaattcctt -ccacaccttccccacacccacacagacctagacgaattccttccacaccttctccacacc -cacacgaacctagacgattccttccacaccttctccatacccacacgaacctagacaatt -ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttccccac -acccacacagacctagacgaattccttccacaccttctccacacccacacgaacctagac -aattccttccacaccttctcacacccacacaaacctagacgaattccttccacaccttct -ccacacccacacaaacctagatgaattccttccacaccttcctcacacccacacgaacct -agacgattccttccacaccttccccacacccacacagacctagacgaattccttccacac -cttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacga -acctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttcca -caccttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccac -acgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcc -ttccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacaccca -cacaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaatt -cttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatt -aattattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccag -gctggagtgcag ->syndip_2_chr20:18208996-18210828 -ggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaat -aaaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgt -atccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccc -acacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctaga -tgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacctt -ccccacacccattctccacacccacacgaacctagacgattccttccacacctccacacc -cacacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgat -tccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcc -acacccacacagacctagacgattccttccacacctccacacccacacgaacctagacga -attccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttct -ccacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacct -agacgattccttccacactttccccacacccacaagaacctagacg-attccttccacac ----ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacaca -aacctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcc -acacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctag -acgattccttccacaccttctccacacccacacacacctagatgaattccttccacacct -tccccacacccacacagacctagacgaattccttccacacattctccacacccacacgaa -cctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccac -accttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacac -gaacctaaacgattccttccacaccttctccacacccacacacacctagatgaattcctt -ccacaccttccccacacccacacagacctagacgaattccttccacaccttctccacacc -cacacgaacctagacgattccttccaca------------ccacacgaacctagacaatt -ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttccccac -acccacacagacctagacgaattccttccacaccttctccacacccacacgaacctagac -aattccttccacaccttctcacacccacacaaacctagacgaattccttccacaccttct -ccacacccacacaaacctagacgaattccttccacaccttcctcacacccacacgaacct -agacgattccttccacaccttccccacacccacacagacctagacgaattccttccacac -cttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacga -acctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttcca -caccttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccac -acgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcc -ttccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacaccca -cacaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaatt -cttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatt -aattattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccag -gctggagtgcag ->p:HG002_1_chr20:18208996-18210828 -ggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaat -aaaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgt -atccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccc -acacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctaga -tgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacctt -ccccacacccattctccacacccacacgaacctagacgattccttccacacctccacacc -cacacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgat -tccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcc -acacccacacagacctagacgattccttccacacctccacacccacacgaacctagacga -attccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttct -ccacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacct -agacgattccttccacactttccccacacccacaagaacctagacg-attccttccacac ----ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacaca -aacctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcc -acacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctag -acgattccttccacaccttctccacacccacacacacctagatgaattccttccacacct -tccccacacccacacagacctagacgaattccttccacacattctccacacccacacgaa -cctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccac -accttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacac -gaacctaaacgattccttccacaccttctccacacccacacacacctagatgaattcctt -ccacaccttccccacacccacacagacctagacgaattccttccacaccttctccacacc -cacacgaacctagacgattccttccaca------------ccacacgaacctagacaatt -ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttccccac -acccacacagacctagacgaattccttccacaccttctccacacccacacgaacctagac -aattccttccacaccttctcacacccacacaaacctagacgaattccttccacaccttct -ccacacccacacaaacctagacgaattccttccacaccttcctcacacccacacgaacct -agacgattccttccacaccttccccacacccacacagacctagacgaattccttccacac -cttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacga -acctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttcca -caccttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccac -acgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcc -ttccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacaccca -cacaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaatt -cttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatt -aattattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccag -gctggagttcag ->p:HG002_2_chr20:18208996-18210828 -ggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaat -aaaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgt -atccttccgtagcttctccacacctacacgaacctagacgattccttccacaccttcccc -acacccacacgaacctagacgattccttccacaccttccccacacccacacgaacctaga -tgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacctt -ccccacacccattctccacacccacacgaacctagacgattccttccacacctccacacc -cacacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgat -tccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcc -acacccacacagacctagacgattccttccacacctccacacccacacgaacctagacga -attccttccacaccttctccacacccacacgaacctagacgaattccttccacaccttct -ccacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacct -agacgattccttccacactttccccacacccacacgaacctagacg-attccttccacac ----ctccacacccacacgaacctagatgaattccttccacaccttccccacacccacaca -aacctagacgattccttccacaccttctccacacccacacaaacctagacaattccttcc -acacacacatgaacctagatgaattccttccacaccttctccacacccacatgaacctag -acgattccttccacaccttctccacacccacacacacctagatgaattccttccacacct -tccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaa -cctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccac -accttctcacacccacacaaacctagatgaattccttccacaccttctccacacccacac -gaacctaaacgattccttccacaccttctccacacccacacacacctagatgaattcctt -ccacaccttccccacacccacacagacctagacgaattccttccacaccttctccacacc -cacacgaacctagacgattccttccacaccttctccatacccacacgaacctagacaatt -ccttccacaccttctcacacccacacaaacctagatgaattccttccacaccttccccac -acccacacagacctagacgaattccttccacaccttctccacacccacacgaacctagac -aattccttccacaccttctcacacccacacaaacctagacgaattccttccacaccttct -ccacacccacacaaacctagatgaattccttccacaccttcctcacacccacacgaacct -agacgattccttccacaccttccccacacccacacagacctagacgaattccttccacac -cttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacga -acctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttcca -caccttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccac -acgaacctagacgattccttccacaccttccccacacccacacagacctagacgaattcc -ttccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacaccca -cacaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaatt -cttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatt -aattattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccag -gctggagtgcag ->ref_chr20:18208996-18210828 -ggtattctttgtactgtttttatttttgcaacttttctgtgtttacagttatttccaaat -aaaaaataagcagaaaggaaaagctaatcatctccccctattccagtcccccaggcatgt -atccttccgtagcttctccacacct----------------------------------- -------acacgaacctagacgattccttccacaccttccccacacccacacgaacctaga -tgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacctt -ccccacacccattctccacacccacacgaacctagacgattccttccacacctccacacc -cacacgaacctagatgaattccttccacaccttccccacacccacacaaacctagacgat -tccttccacaccttctccacacccacacgaacctagacgaattccttccagaccttctcc -acacccacacagacctagacgattccttccacacctccacacccacacgaacctagacga -attccttccacaccttgtgcacacccacacgaacctagacgaattccttccacaccttct -ccacacccacacgaacctagacgaattccttccacaccttctccacacccacacgaacct -agacgattccttccacaccttccccacacccacacagacctagacgaattccttgcacac -cttctccacacccacacgaacctagacgaattccttccacaccttctccatacccacacg -aacctagacaattccttccacaccttct-------------------------------c -acacccacacaaacctagatgaattccttccacaccttctccacacccacacgaacctaa -acgattccttccacaccttctccacacccacacacacctagatgaattccttccacacct -tccccacacccacacagacctagacgaattccttccacaccttctccacacccacacgaa -cctagacgattccttccacaccttctccatacccacacgaacctagacaattccttccac -accttctcacacccacacaa---------------------------------------- --------------------------------------------acctagatgaattcctt -ccacaccttccccacacccacacagacctagacgaattccttccacaccttctccacacc -cacacgaacctagacg-------------------------------------------- ------------------------------------------------------------- ---------------------attccttccacaccttccccacacccacacgaacctagac -aattccttgcacaccttctcacacccacacaaacctagacgaattccttccacaccttct -ccacacccacacaaacctagacgaattccttccacaccttcctcacacccacacgaacct -agacgattccttccacaccttccccacacccacacagacctagacgaattccttccacac -cttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacga -acctagacaattccttccacaccttctcacacccacacaaacctagatgaattccttcca -caccttctccacacccacacaaacctagacgaattccttccacaccttcctcacacccac -acgaacctagatgattccttccacaccttccccacacccacacagacctagacgaattcc -ttccacaccttcctaacacccacacgaacctagagaattccttccacaccttcacaccca -cacaaacctagacgaattccttccacaccttctccacacccacacaaacctagacaaatt -cttatacacttaaaatgggattttgttgttttattaaaatgcagtcattctctatgcatt -aattattgtgcagcttgatttttctcctttttttttgttaaatcttcctccgtcatccag -gctggagtgcag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e47b8fad37392ee138dfca4c2353754.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9e47b8fad37392ee138dfca4c2353754.msa deleted file mode 100644 index 1b7c4215..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e47b8fad37392ee138dfca4c2353754.msa +++ /dev/null @@ -1,195 +0,0 @@ ->syndip_1_chr20:61100692-61102787 -ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca -gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac -tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc -ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg -tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac -acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct -ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag -agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac -cccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccg -agtgagggcagatggccacatcctctacttcctgtgtcacacct---------------- ------------------------------------------------------------- -------------------------------------ggggagaccctgagtgagggcaga -cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagc -cacctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacggccacg -tcttctacttcctgtgtcacacctggagagaccccgagtgagggtggatggccacatcct -ctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctac -ttcctgtgtcacacctggagagaccccgagtgagggcagactgccacctcctctacttcc -tgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtg -ccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcac -acctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct -ggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag -agaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagac -cccgagtgagggcagatggccacatcctctaattcctatgtcacacctggagagaccccg -agtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtg -agggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg -cagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcaga -cagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagc -taccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacc -tcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcct -ctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctat -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc -tgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgtg -tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac -acctggggagaccccgagtgagggcagatggccacatcctctaattcctgtgtcacacct -ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag -acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg -tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgta ->syndip_2_chr20:61100692-61102787 -ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca -gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac -tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc -ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg -tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac -acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct -ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag -agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac -tccaagtgaggagagacggccacgtcttctacttcctgtgtcacacctggagagacctcg -agtgagggcagatggccacatcctctaattcctgtgtcacacctggagaaaccccaagtg -agggcagactgccacctcctctacttcctgtgtcacacctagagagaccccgagtgagga -cagccagccatgtcctctacttcctgtgccacatccggagagatcccgagtgagggcaga -cagccatgtcctctacttcctgtgtcacacctggagagaccccgagtgagggcagacagc -cacatcctctaattcctgtgtcacacctggagagaccccgagtgagggcagacggctaca -tcctctaattcctgtgtcatgcctggagagaccccgagtgagggcagatggccacatcct -ctaattcctatgtcacacctggagagaccccgagtgagggtggatggccacatcctctaa -ttcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctacttcc -tgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtcctgtg -ccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgtgtcac -acctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtcacacct -ggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag -agaccccgagtgagggcagacggccacatcctctatttcctgtgtcacacctggagagac -cccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagagaccccg -agtgaaggcagaaggccacatcctctacttcctgtgtcacacctagagagaccccgagtg -agggcggatggccacatcctctaattcctatgtcacacctggagagaccccgagtgaggg -tggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcaga -tggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagc -catgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctacc -ccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctctt -ctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctac -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc -tgtgtcacacatggagagaccctgagtgagggcagaaggccacatcctctacttcctgtg -tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac -acctggggagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct -ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag -acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg -tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgta ->p:HG002_1_chr20:61100692-61102787 -ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca -gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac -tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc -ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg -tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac -acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct -ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag -agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac -tccaagtgaggagagacggccacgtcttctacttcctgtgtcacacctggagagacctcg -agtgagggcagatggccacatcctctaattcctgtgtcacacctggagaaaccccaagtg -agggcagactgccacctcctctacttcctgtgtcacacctagagagaccccgagtgagga -cagccagccatgtcctctacttcctgtgccacatccggagagatcccgagtgagggcaga -cagccatgtcctctacttcctgtgtcacacctggagagaccccgagtgagggcagacagc -cacatcctctaattcctgtgtcacacctggagagaccccgagtgagggcagacggctaca -tcctctaattcctgtgtcatgcctggagagaccccgagtgagggcagatggccacatcct -ctaattcctatgtcacacctggagagaccccgagtgagggtggatggccacatcctctaa -ttcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctacttcc -tgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtcctgtg -ccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgtgtcac -acctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtcacacct -ggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag -agaccccgagtgagggcagacggccacatcctctatttcctgtgtcacacctggagagac -cccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagagaccccg -agtgaaggcagaaggccacatcctctacttcctgtgtcacacctagagagaccccgagtg -agggcggatggccacatcctctaattcctatgtcacacctggagagaccccgagtgaggg -tggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcaga -tggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacagc -catgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctacc -ccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctctt -ctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctctac -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc -tgtgtcacacatggagagaccctgagtgagggcagaaggccacatcctctacttcctgtg -tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac -acctggggagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct -ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag -acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg -tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgta ->p:HG002_2_chr20:61100692-61102787 -ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca -gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac -tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc -ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg -tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac -acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct -ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag -agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac -cccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccg -agtgagggcagatggccacatcctctacttcctgtgtcacacct---------------- ------------------------------------------------------------- -------------------------------------ggggagaccctgagtgagggcaga -cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagc -cacctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacggccacg -tcttctacttcctgtgtcacacctggagagaccccgagtgagggtggatggccacatcct -ctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctac -ttcctgtgtcacacctggagagaccccgagtgagggcagactgccacctcctctacttcc -tgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtg -ccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcac -acctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct -ggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag -agaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagac -cccgagtgagggcagatggccacatcctctaattcctatgtcacacctggagagaccccg -agtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtg -agggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg -cagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcaga -cagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagc -taccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacc -tcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcct -ctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctat -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc -tgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgtg -tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac -acctggggagaccccgagtgagggcagatggccacatcctctaattcctgtgtcacacct -ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag -acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg -tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgta ->ref_chr20:61100692-61102787 -ttggtacatgtacagattgtgcaagacaataggacaccagacagatccccgggctccaca -gcagaagtctggttactgggcaggcaggccccaaacactgtatttaaaacaaaaccccac -tgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacatc -ctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgtg -tcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtcac -acctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacct -ggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccggag -agaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagagac -cccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagaccccg -agtgagggcagatggccacatcctctacttcctgtgtcacacct---------------- ------------------------------------------------------------- -------------------------------------ggggagaccctgagtgagggcaga -cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagc -cacctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacggccaca -tcttctacttcctgtgtcacacctggagagacctcgagtgagggcagatggccacatcct -ctaa-------------------------------------------------------- -ttcctgtgtcacacctggagagaccccaagtgagggcagactgccacctcctctacttcc -tgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgtg -ccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtcac -acctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacct -ggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctggag -agaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagagac -cccgagtgagggcatatggccacatcctctaattcctatgtcacacctggagagaccccg -agtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtg -agggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgaggg -cagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcaga -cagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagc -taccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacc -tcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcct -ctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctat -ttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattcc -tgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgtg -tcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtcac -acctggggagaccccgagtgagggcagatggccacatcctctaattcctgtgtcacacct -ggagacacacagagtaaaggtggacagccacctcctctacgtcctgtgccacacctggag -acaccctgagttaaggcagatggccacctcctctaattatttttaagaacttttttgggg -tataatttacatgccagaaagttcacccatttcaagcatatgattcaatattaaagctta -aaaatgttatcaatttaataacattgatggttacagagctgtgta diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e8a807906028744f45dff50046a00aa.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9e8a807906028744f45dff50046a00aa.msa deleted file mode 100644 index ea31e8a0..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9e8a807906028744f45dff50046a00aa.msa +++ /dev/null @@ -1,190 +0,0 @@ ->syndip_1_chr20:20337100-20337807 -tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg -aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac -tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat -ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat -gggtggatggatagatgggtggatggataaatggatggatggatggatggatagatgggt -gggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggt -gggtggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat -ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat -ggatagatgtgtgggtggatggatggatggatggatggatggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatggatggatggatggatggatggatagat -gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatggatggatggatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -ggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt -ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt -cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt -tacaatcctgcctgcctctcacccagacctctt ->syndip_2_chr20:20337100-20337807 -tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg -aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac -tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat -ggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatggat -agatgggtggatggataaatggatgg----atggatggatggatagatgggtgggtggat -ggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat -ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat -ggatagatgggtgggtggatggatggatggatggatggatggatagatggataga----- ------------tgggtgggtggatggatggatggatggatggatggatggatggatagat -gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtggg----tggatggatggatggatggatggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggata--------------------gatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggataga--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------tgggtgggtgggtggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt -ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt -cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt -tacaatcctgcctgcctctcacccagacctctt ->p:HG002_1_chr20:20337100-20337807 -tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg -aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac -tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat -ggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatggat -agatgggtggatggataaatggatgg----atggatggatggatagatgggtgggtggat -ggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat -ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat -ggatagatgggtgggtggatggatggatggatggatggatggatagatggataga----- ------------tgggtgggtggatggatggatggatggatggatggatggatggatagat -gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtggg----tggatggatggatggatggatggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggata--------------------gatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggataga--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------tgggtgggtgggtggatggatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt -ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt -cttagcagacgtcccaccatggaagaggtcatggggcacaggggctttgggaaaggtgtt -tacaatcctgcctccctctcacccagacctctt ->p:HG002_2_chr20:20337100-20337807 -tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg -aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac -tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat -ggatggatggatggatggatggatggatagatgggtgggtggatggatggatggatagat -gggtggatggatagatgggtggatggataaatggatggatggatggatggatagatgggt -gggtggatggatggatggatggatggatggatggatggatggatagatggatagatgggt -gggtggatggatggatggatggatggatggatggatggatggatagatgggtgggtggat -ggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggt -ggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatggat -ggatagatgtgtgggtggatggatggatggatggatggatggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatggatggatggatggatggatggatagat -gggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatggatagatgggtgggtggatggatggatggatagat -gggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatgggtgggtggatggatggatggatggatggatggatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatggat -ggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggat -ggatggatggatagatggatagatgggtgggtggatggatggatggatagatggatagat -gggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggt -gggtggatggatggatggatagatgggtgggtggatggatggatggatggatggatagat -ggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggat -ggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatggat -agatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggat -ggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggat -ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggt -ggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgggt -ggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgtt -cttagcagacgtcccaccatggaagaggtcatggggcacaggggctttgggaaaggtgtt -tacaatcctgcctccctctcacccagacctctt ->ref_chr20:20337100-20337807 -tacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagagg -aagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctcac -tagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtggat -ggatggatggatagatggatggatggatggatggatggatggatggatggatggatggat -agatgggtgggtgg----gtggatgg----atggatggatggatggatggatggatggat -ggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggat -ggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggataaat -ggatggatggatggatggatagatgggtgggtggatggatggatggatggatggatggat -ggatggatagat------------------gtgggtggatggatggatggatagatgggt -gggtgggtggatggatggatggatggatagatgggtgggtgggtggatggatggatggat -ggatagaataaaaaagaaa----------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------gctaggacatggttctagtgtt -cttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgtt -tacaatcctgcctgcctctcacccagacctctt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9ed8d97b4b4c931bed6d1168b8d47c65.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9ed8d97b4b4c931bed6d1168b8d47c65.msa deleted file mode 100644 index 42ffb9c5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9ed8d97b4b4c931bed6d1168b8d47c65.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:63048932-63049513 -agcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcc -aggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtca -tgtgggggcagactcctcctcctcctcctcttcctcctcc-------------------- --------tcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctc -ctcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttccttctc -ctcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctc -ttcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctc -ctcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttcctcttcctc -ctcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcttcctc -ctcc---------------------------------------tcttcctctttctcctc -ctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctc -ctcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctc -ttcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttc -ctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctc -ctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct-cctcctcttcct -cctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctc -ttcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcc -tcccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttcca -ggacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgacca -ctggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggc -aggacccagaagcctggtagaaagtgaccatgtgtggcaggt ->syndip_2_chr20:63048932-63049513 -agcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcc -aggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtca -tgtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctc -ttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttcctcctc -ctcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctc -tttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctc -ctcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttcctcttcctc -ctcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcctcttc -ctcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctc -ttcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcctcctcctc -ctcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctc -ctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttc -ctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttc -ctcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctc -ctcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcct-cctcctcttcct -cctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctc -ttcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcc -tcccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttcca -ggacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgacca -ctggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggc -aggacccagaagcctggtagaaagtgaccatgtgtggcaggt ->p:HG002_1_chr20:63048932-63049513 -agcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcc -aggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtca -tgtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctc -ttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttcctcctc -ctcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctc -tttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctcctcttcctc -ctcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttcctcttcctc -ctcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcctcttc -ctcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctccttctcctc -ttcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctcctcctcctc -ctcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctc -ctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctcctcttcttc -ctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcttc -ctcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctc -ctcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcct-cctcctcttcct -cctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctc -ttcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcc -tcccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttcca -ggacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgacca -ctggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggc -aggacccagaagcctggtagaaagtgaccatgtgtggcaggt ->p:HG002_2_chr20:63048932-63049513 -agcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcc -aggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtca -tgtgggggcagactcctcctcctcctcctcttcctcctcc-------------------- --------tcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctc -ctcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctcttccttctc -ctcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttcctcctcctc -ttcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctc -ctcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttcctcttcctc -ctcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttcctcttcctc -ctcc---------------------------------------tcttcctctttctcctc -ctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctc -ctcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctc -ttcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttc -ctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctc -ctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcct-cctcctcttcct -cctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctc -ttcctcctcctcctcttcctcccctcctcctcctcctcttcctcctcctcctcctcttcc -tcccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttcca -ggacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgacca -ctggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggc -aggacccagaagcctggtagaaagtgaccatgtgtggcaggt ->ref_chr20:63048932-63049513 -agcttgtttggacctgaagaccagcctgagcgaggagagtcttgtgcagacggtttatcc -aggaggagcccggggagaggggggtgggaaaagccacagttttggaggtcagcaaggtca -tgtgggggcaga------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------ctcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctc -ttcctcttcctcctcctcctcctcttcctcctcctcctcctcttcctccctcctcttcct -cctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcctcctcctc -ttcctcctcctcctcttcctctcctcctcctcctcctcttcctcctcctcctcctcttcc -tcccctcctcctcctcttcctcctcgtcctcttcctccttctgccaggacccttcttcca -ggacccctgagaagcgcatagaatagcgtccaggactgtctgccccaggcacgctgacca -ctggctccactcccctgggcaagggtcgcccctgggctgctgcctcccagcgacacaggc -aggacccagaagcctggtagaaagtgaccatgtgtggcaggt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_9f37ee6609b29133db4005435bacd6b0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_9f37ee6609b29133db4005435bacd6b0.msa deleted file mode 100644 index 523a967e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_9f37ee6609b29133db4005435bacd6b0.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:60702895-60703197 -tgatggcacaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatat -taccaacatttgtcattgtctttctttcttttctttctctctctctctttcttttccttc -tttctttctttctttctttctttctttctttctttctttctttctttctttcttttcttt -ccttcttctttctttctttctttctttctttctttctttctttctttctttctttctttc -tttctttctttctttctttctttcttctttctttctttttctttcttttttttttgggat -ggagtctcgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatc -tccacctcccaggttcaagcgattgaactcactgcc ->syndip_2_chr20:60702895-60703197 -tgatggcacaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatat -taccaacatttgtcattgtctttctttcttttctttctctctctctctttcttttccttc -tttctttctttctttctttctttcttc--------------------------------- --------ctttctttctttctttctttctttctttctttctttctttcttt--------- -----------------tctttccttctttctttctttctttctttctttttttttgggat -ggagtctcgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatc -tccacctcccaggttcaagcgattgaactcactgcc ->p:HG002_1_chr20:60702895-60703197 -tgatggcacaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatat -taccaacatttgtcattgtctttctttcttttctttctctctctctctttctttcttttc -cttctttctttctttctttctttcctt--------------------------------- --------ctttctttctttctttctttctttctttctttctttctttcttt--------- -----------------tctttccttctttctttctttctttctttctttttttttgggat -ggagtctcgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatc -tccacctcccaggttcaagcgattgaactcactgcc ->p:HG002_2_chr20:60702895-60703197 -tgatggcacaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatat -taccaacatttgtcattgtctttctttcttttctttctctctctctctttcttttccttc -tttctttctttctttctttctttctttctttctttctttctttctttctttcttttcttt -ccttcttctttctttctttctttctttctttctttctttctttctttctttctttctttc -tttctttctttctttctttctttcttcttctttctttctttctttctttttttttgggat -ggagtctcgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatc -tccacctcccaggttcaagcgattgaactcactgcc ->ref_chr20:60702895-60703197 -tgatggcacaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatat -taccaacatttgtcattgtctttctttcttttctttctctctctctctttcttttcctt- ------------------------------------------------------------- --------ctttctttctttctttctttctttctttctttctttctttcttt--------- -----------------tctttccttctttctttctttctttctttctttttttttgggat -ggagtctcgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatc -tccacctcccaggttcaagcgattgaactcactgcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a09dd6a3c937eb8b429c7e2fe04ca66e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a09dd6a3c937eb8b429c7e2fe04ca66e.msa deleted file mode 100644 index 2abca84a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a09dd6a3c937eb8b429c7e2fe04ca66e.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:63027896-63028267 -gacggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgt -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggt -ggggagaggaccggtggggagggggccggtggagagggggccggtggggagggggccggt -ggggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtg -gggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtggg -gagggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtggg -gagggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggg -agggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggagg -gggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagc -gtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgc -agcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc ->syndip_2_chr20:63027896-63028267 -gacggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgt -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggt -gggga----------------ggggccggtggagagggggccggtggggagggggccggc -ggggag--------------tggtttggtggggagggggccggtggggagggggcctgcg -gggaggggccggtggggag-----------------------------ggggccggtggg -gagggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtggg -gag-----------------------------ggggccggtggggagggggccggcgggg -agggggccggcggggaggggccggtggggagtggtctg---------------------- ---------------------gtggggagggggccggtggggaggaggctggtgaagtagc -gtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgc -agcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc ->p:HG002_1_chr20:63027896-63028267 -gacggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgt -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggt -gggga----------------ggggccggtggagagggggccggtggggagggggccggc -ggggag--------------tggtttggtggggagggggccggtggggagggggcctgcg -gggaggggccggtggggag-----------------------------ggggccggtggg -gagggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtggg -gag-----------------------------ggggccggtggggagggggccggcgggg -agggggccggcggggaggggccggtggggagtggtctg---------------------- ---------------------gtggggagggggccggtggggaggaggctggtgaagtagc -gtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgc -agcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc ->p:HG002_2_chr20:63027896-63028267 -gacggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgt -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggt -ggggagaggaccggtggggagggggccggtggagagggggccggtggggagggggccggt -ggggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtg -gggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtggg -gagggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtggg -gagggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggg -agggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggagg -gggccggtgggggggggcctgcagggagggggccggtggggaggaggctggtgaagtagc -gtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgc -agcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc ->ref_chr20:63027896-63028267 -gacggaccagcatctatcatggctgttttgcgtttcttgatttcacgatgtctgttgtgt -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggt -gggga----------------ggggccggtggagagggggccggtggggagggggccggc -ggggag--------------tggttt---------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------ggtggggaggaggctggtgaagtagc -gtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctgc -agcttcatcaggttctcaattagcggagggcgctggcggtggaggagggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a1254d6e13443b8d2412a3c3c0fef3fe.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a1254d6e13443b8d2412a3c3c0fef3fe.msa deleted file mode 100644 index c0049b7e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a1254d6e13443b8d2412a3c3c0fef3fe.msa +++ /dev/null @@ -1,205 +0,0 @@ ->syndip_1_chr20:16257744-16259315 -tgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaagag -acacaccccttccccatcccaaagagacacaccccttccccatcccaaagagacacaccc -cttccccatcccaaacacacacaccccttccccatcccaaacacacacaccccttcccca -tcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatcctaaac -acacacacaccttgccttcgcaaacacacacaccccttccccatcacaaacacacacacc -ctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccccat -gccaaacacacacaacccttccccaattctaaacacacacacctcttccccatcccaaac -acaaacaccccttccccatcccaaacacacccaccctttcctgcatgccaaacacccaca -ccccttccccatcccaaacacacaccccatccccaattccaaacacacacaccccttccc -catcccaaacacacacaccccttccacatgagaaacacacacaccccttctcatcccaaa -cacaaacacacccattccccatcacaaacacacgcaccccttccccatcccaaacacaca -caccccttcccca--------------------------attgtaaacacacacacccct -tccccatcccaaacacacaccccccttccccatcccaaacacacaccccccttccccatc -ccaaacacacccaccccttcccacatcccaaacacacacaccccttccctatcccaaaca -cacactccatccccaattccaaacacacacaccccttccccatcccaaacacacacaccc -cttcccccatcccaaacgcacacaccccttccctatcccaaacacacaccccttcccttt -ccaaaacacacccatcccttccccatcccaaacacacacaacccttcccatcccagacac -acccaccccttcccatctcaaatacacgcaacccttccccatcccaaacacacacaccta -ttccccatccgaaacacacacaccccttcctcatcccacacacacccattccccatccca -gacacacccatcccttccccatactaaacacaaccaccccttccccatcccacacacaca -caccccttccccaattccaaacacacacaccccttccccattcaaaacacacgcacccct -tcccatctgaaacacacccactccttcccatctgaaacacacccactccttcccatccca -aacacacccactccttcccatcccaaacacacacaccccttccccatcccaaaaacacac -accctttcgcaatcccaaatacacaagccccttcccaaattccacacacacacacctctt -ccccatcccaaacaaacccaccctttccccattcgaaacacacacaccccttctccaatt -ccaaacacacacaccccttcccatcacaaacacacacacaccttccacatcccaaataca -cacaccccttcccatctcaaacacacacatcccttccccaattccaaaaacacacacccc -ttccccatcccaaacacccccaccccttcccatccccaaacacacacccctttcccatcc -caaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaaacac -acataccccttcccatcccaaagacacacactcattctgcatcccaaacacacacacccc -ttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccccatc -ccaaacacatacaccccttccccatcgccaacacacacaccccttccccatcccaaacac -acacacccctttccatcccaaacacacacccattccccatcccagacacacccacccgtt -ccccatcccagacacacacaacccttccccaattccaaacacacaccccttcccatccca -aacacacacacccatttcccatcccagacacatccaccccttccacaactctgaacaccc -accccttccccatcccaaacacacacaccccttccccatcccaaacacacacacccattc -cccatcccaaacacacacacccattccccatcccaaacacaaccaccccttccccatccc -aaacacacacaccccttccccatcccaaacacacacaca--------------------- -----ccttccccatcccaaacacacccacccttactccatctcaaacatgtacacccctt -cccctatcccaaaatacacacatccatccctacacaccctcacccatttcccca ->syndip_2_chr20:16257744-16259315 -tgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaagag -acacaccccttccccatcccaaagagacacaccccttccccatcccaaagag-------- -------------------acacaccccttccccatcccaaacacacacaccccttcccca -tcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatcctaaac -acacacacaccttgccttcgcaaacacacacaccccttccccatcacaaacacacacacc -ctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccccat -gccaaacacacacaacccttccccaattctaaacacacacacctcttccccatcccaaac -acaaacaccccttccccatcccaaacacacccaccctttcctgcatgccaaacacccaca -ccccttccccatcccaaacacacaccccatccccaattccaaacacacacaccccttccc -catcccaaacacacacaccccttccacatgagaaacacacacaccccttctcatcccaaa -cacaaacacacccattccccatcacaaacacacgcaccccttccccatcccaaacacaca -caccccttccccatcccaaacacacacaccccttccccaattctaaacacacacacccct -tccccatcccaaacacacaccccccttccccatcccaaacacacaccccccttccccatc -ccaaacacacccaccccttcccacatcccaaacacacacaccccttccctatcccaaaca -cacactccatccccaattccaaacacacacaccccttccccatcccaaacacacacaccc -cttcccccatcccaaacgcacacaccccttccctatcccaaacacacaccccttcccttt -ccaaaacacacccatcccttccccatcccaaacacacacaacccttcccatcccagacac -acccaccccttcccatctcaaatacacgcaacccttc----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------cccatcccaaacacacacaccccttccccatcccaaaaacacac -accctttcgcaatcccaaatacacaagccccttcccaaattccacacacacacacctctt -ccccatcccaaacaaacccaccctttccccattgtaaacacacacaccccttctccaatt -ccaaacacacacaccccttcccatcacaaacacacacacaccttccacatcccaaataca -cacaccccttcccatctcaaacacacacatcccttccccaattccaaaaacacacacccc -ttccccatcccaaacacccccaccccttcccatccccaaacacacacccctttcccatcc -caaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaaacac -acataccccttcccatcccaaagacacacactcattctgcatcccaaacacacacacccc -ttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccccatc -ccaaacacatacaccccttccccatcgccaacacacacaccccttccccatcccaaacac -acacacccctttccatcccaaacacacacccattccccatcccagacacacccacccgtt -ccccatcccagacacacacaacccttccccaattccaaacacacaccccttcccatccca -aacacacacacccatttcccatcccagacacatccaccccttccacaactctgaacaccc -accccttccccatcccaaacacacacaccccttccccatcccaaacacacacacccattc -cccatcccaaacacacacacccattccccatcccaaacacaaccaccccttccccatccc -aaacacacacaccccttccccatcccaaacacacacacaccttcccatcccaaacacaca -caccccttccccatcccaaacacacccacccttactccatctcaaacatgtacacccctt -cccctatcccaaaatacacacatccatccctacacaccctcacccatttcccca ->p:HG002_1_chr20:16257744-16259315 -tgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaagag -acacaccccttccccatcccaaagagacacaccccttccccatcccaaagag-------- -------------------acacaccccttccccatcccaaacacacacaccccttcccca -tcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatcctaaac -acacacacaccttgccttcgcaaacacacacaccccttccccatcacaaacacacacacc -ctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccccat -gccaaacacacacaacccttccccaattctaaacacacacacctcttccccatcccaaac -acaaacaccccttccccatcccaaacacacccaccctttcctgcatgccaaacacccaca -ccccttccccatcccaaacacacaccccatccccaattccaaacacacacaccccttccc -catcccaaacacacacaccccttccacatgagaaacacacacaccccttctcatcccaaa -cacaaacacacccattccccatcacaaacacacgcaccccttccccatcccaaacacaca -caccccttcccca----------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------attgtaaacacacacaccccttctccaatt -ccaaacacacacaccccttcccatcacaaacacacacacaccttccacatcccaaataca -cacaccccttcccatctcaaacacacacatcccttccccaattccaaaaacacacacccc -ttccccatcccaaacacccccaccccttcccatccccaaacacacacccctttcccatcc -caaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaaacac -acataccccttcccatcccaaagacacacactcattctgcatcccaaacacacacacccc -ttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccccatc -ccaaacacatacaccccttccccatcgccaacacacacaccccttccccatcccaaacac -acacacccctttccatcccaaacacacacccattccccatcccagacacacccacccgtt -ccccatcccagacacacacaacccttccccaattccaaacacacaccccttcccatccca -aacacacacacccatttcccatcccagacacatccaccccttccacaactctgaacaccc -accccttccccatcccaaacacacacaccccttccccatcccaaacacacacacccattc -cccatcccaaacacacacacccattccccatcccaaacacaaccaccccttccccatccc -aaacacacacaccccttccccatcccaaacacacacaca--------------------- -----ccttccccatcccaaacacacccacccttactccatctcaaacatgtacacccctt -cccctatcccaaaatacacacatccatccctacacaccctcacccatttcccca ->p:HG002_2_chr20:16257744-16259315 -tgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaagag -acacaccccttccccatcccaaagagacacaccccttccccatcccaaagagacacaccc -cttccccatcccaaacacacacaccccttccccatcccaaacacacacaccccttcccca -tcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatcctaaac -acacacacaccttgccttcgcaaacacacacaccccttccccatcacaaacacacacacc -ctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccccat -gccaaacacacacaacccttccccaattctaaacacacacacctcttccccatcccaaac -acaaacaccccttccccatcccaaacacacccaccctttcctgcatgccaaacacccaca -ccccttccccatcccaaacacacaccccatccccaattccaaacacacacaccccttccc -catcccaaacacacacaccccttccacatgagaaacacacacaccccttctcatcccaaa -cacaaacacacccattccccatcacaaacacacgcaccccttccccatcccaaacacaca -caccccttcccca--------------------------attgtaaacacacacacccct -tccccatcccaaacacacaccccccttccccatcccaaacacacaccccccttccccatc -ccaaacacacccaccccttcccacatcccaaacacacacaccccttccctatcccaaaca -cacactccatccccaattccaaacacacacaccccttccccatcccaaacacacacaccc -cttcccccatcccaaacgcacacaccccttccctatcccaaacacacaccccttcccttt -ccaaaacacacccatcccttccccatcccaaacacacacaacccttcccatcccagacac -acccaccccttcccatctcaaatacacgcaacccttccccatcccaaacacacacaccta -ttccccatccgaaacacacacaccccttcctcatcccacacacacccattccccatccca -gacacacccatcccttccccatactaaacacaaccaccccttccccatcccacacacaca -caccccttccccaattccaaacacacacaccccttccccattcaaaacacacgcacccct -tcccatctgaaacacacccactccttcccatctgaaacacacccactccttcccatccca -aacacacccactccttcccatcccaaacacacacaccccttccccatcccaaaaacacac -accctttcgcaatcccaaatacacaagccccttcccaaattccacacacacacacctctt -ccccatcccaaacaaacccaccctttccccattcgaaacacacacaccccttctccaatt -ccaaacacacacaccccttcccatcacaaacacacacacaccttccacatcccaaataca -cacaccccttcccatctcaaacacacacatcccttccccaattccaaaaacacacacccc -ttccccatcccaaacacccccaccccttcccatccccaaacacacacccctttcccatcc -caaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaaacac -acataccccttcccatcccaaagacacacactcattctgcatcccaaacacacacacccc -ttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccccatc -ccaaacacatacaccccttccccatcgccaacacacacaccccttccccatcccaaacac -acacacccctttccatcccaaacacacacccattccccatcccagacacacccacccgtt -ccccatcccagacacacacaacccttccccaattccaaacacacaccccttcccatccca -aacacacacacccatttcccatcccagacacatccaccccttccacaactctgaacaccc -accccttccccatcccaaacacacacaccccttccccatcccaaacacacacacccattc -cccatcccaaacacacacacccattccccatcccaaacacaaccaccccttccccatccc -aaacacacacaccccttccccatcccaaacacacacaca--------------------- -----ccttccccatcccaaacacacccacccttactccatctcaaacatgtacacccctt -cccctatcccaaaatacacacatccatccctacacaccctcacccatttcccca ->ref_chr20:16257744-16259315 -tgaaatcagatatcatacccacaccccaaaacacacacactccttccccatcccaaagag -acacaccccttccccatcccaaagagacacaccccttccccatcccaaagagacacaccc -cttccccatcccaaacacacacaccccttccccatcccaaacacacacaccccttcccca -tcccaaacacacacacccctttcccatcccaaacacacacacccattgcccatcctaaac -acacacacaccttgccttcgcaaacacacacaccccttccccatcacaaacacacacacc -ctttccctatcccatgcacacacaccttccacttcccaaacacacacaccccttccccat -gccaaacacacacaacccttccccaattctaaacacacacacctcttccccatcccaaac -acaaacaccccttccccatcccaaacacacccaccctttcctgcatgccaaacacccaca -ccccttccccatcccaaacacacaccccatccccaattccaaacacacacaccccttccc -catcccaaacacacacaccccttccacatgagaaacacacacaccccttctcatcccaaa -cacaaacacacccattccccatcacaaacacacgcaccccttccccatcccaaacacaca -caccccttcccca----------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------attgtaaacacacacaccccttctccaatt -ccaaacacacacaccccttcccatcacaaacacacacacaccttccacatcccaaataca -cacaccccttcccatctcaaacacacacatcccttccccaattccaaaaacacacacccc -ttccccatcccaaacacccccaccccttcccatccccaaacacacacccctttcccatcc -caaatacacaaaccccttccctaattccacacacacacaccccttccccatcccaaacac -acataccccttcccatcccaaagacacacactcattctgcatcccaaacacacacacccc -ttcccatcccaaacacacacactacctccgcatcccaaacacatataccccttccccatc -ccaaacacatacaccccttccccatcgccaacacacacaccccttccccatcccaaacac -acacacccctttccatcccaaacacacacccattccccatcccagacacacccacccgtt -ccccatcccagacacacacaacccttccccaattccaaacacacaccccttcccatccca -aacacacacacccatttcccatcccagacacatccaccccttccacaactctgaacaccc -accccttccccatcccaaacacacacaccccttccccatcccaaacacacacacccattc -cccatcccaaacacacacacccattccccatcccaaacacaaccaccccttccccatccc -aaacacacacaccccttccccatcccaaacacacacaca--------------------- -----ccttccccatcccaaacacacccacccttactccatctcaaacatgtacacccctt -cccctatcccaaaatacacacatccatccctacacaccctcacccatttcccca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a1f538b067e21838ec0bc49e159f481d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a1f538b067e21838ec0bc49e159f481d.msa deleted file mode 100644 index fda94bce..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a1f538b067e21838ec0bc49e159f481d.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:62875131-62875514 -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagccccgcaccctcacctgcaccctcacccccacccccacccccaccccca -cccccacccccacccgcacccccacccccacccgcacccccacccccacccccacccgca -cccccacccccacccccacccgcacccccacccccacccgcacccccacccccaccccca -cccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgca -cccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccg-- -----------------cacccgcacccccacccccaccctcacccgcacccgcaccccca -cccccacccccacccgcacccgcacccccacccccacccccacccccacccccacccgca -cccgcacccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgca -cccccacccgcacccccacccccacccccacccccacccgcacccgcacccccaccccca -cccccacccccacccccacccccacccccacccccaccctcacccgcacccccaccctca -cccccaccctcccccccacccgcacccgcacccccaccctcacccgcacccccaccctca -cccccaccctcacccccaccctcacccccacccccaccctcacccgcacccgcaccccca -ccctcacccccacccccacccccaccctcaccctcaccctcacccgcacccgcaccccca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcaccctcactcgcaccgcaccctcactggcaccctcacccacac ->syndip_2_chr20:62875131-62875514 -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagccccgcaccctcacctgcaccctcacccccacccccacccccaccccca -cccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgca -cccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgca -cccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcaccccca -cccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgca -cccccacccccacccccacccgcacccccacccccacccccacccgcacccgcaccccca -cccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcaccccca -cccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgca -cccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgca -cccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcaccccca -ccctcacccccaccctcacccgcacccccacccccacccccacccccaccctccccccca -cccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcaccccca -ccctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcaccctcactcgcaccgcaccctcactggcaccctcacccacac ->p:HG002_1_chr20:62875131-62875514 -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagccccgcaccctcacctgcaccctcacccccacccccacccccaccccca -cccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgca -cccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgca -cccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcaccccca -cccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgca -cccccacccccacccccacccgcacccccacccccacccccacccgcacccgcaccccca -cccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcaccccca -cccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgca -cccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgca -cccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcaccccca -ccctcacccccaccctcacccgcacccccacccccacccccacccccaccctccccccca -cccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcaccccca -ccctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcaccctcactcgcaccgcaccctcactggcaccctcacccacac ->p:HG002_2_chr20:62875131-62875514 -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagccccgcaccctcacctgcaccctcacccccacccccacccccaccccca -cccccacccgcacccccacccccacccccacccgcacccccacccccacccccacccgca -cccccacccccacccccacccgcacccccacccccacccgcacccccacccccaccccca -cccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgca -cccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccg-- -----------------cacccgcacccccacccccaccctcacccgcacccgcaccccca -cccccacccccacccgcacccgcacccccacccccacccccacccccacccccacccgca -cccgcacccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgca -cccccacccgcacccccacccccacccccacccccacccgcacccgcacccccaccccca -cccccacccccacccccacccccacccccacccccaccctcacccgcacccccaccctca -cccccaccctcacccccaccctcacccgcaccctcacccgcacccgcaccctccccccca -cccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcaccccca -ccctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcaccctcactcgcaccgcaccctcactggcaccctcacccacac ->ref_chr20:62875131-62875514 -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagccccgcaccctcacctgcaccctcacccccacccccacccccaccccca -cccccacccgcacccccacccccaccctcccccccacccgcacccgcacccccaccctca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcacccccactcgcacccgcacccccaccctcacccgcacccccaccctcaccccca -ccctcacccccaccctcacccccacccccaccctcacccgcaccctcactcgca------ --------------------ccgcaccctcactggcaccctcacccacac----------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a3215e6d9db793005f49da3d52d4fbc8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a3215e6d9db793005f49da3d52d4fbc8.msa deleted file mode 100644 index 36e780f5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a3215e6d9db793005f49da3d52d4fbc8.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:13848063-13848750 -atctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggca -gaggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaatt -gcgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaa -gagagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagg -agaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga -agaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaa -gaagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaaga -agtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggag -gaagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaa -gaagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaag -acaaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttaca -ctctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcc -agagaatc ->syndip_2_chr20:13848063-13848750 -atctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggca -gaggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaatt -gcgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaa -gagagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagg -agaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga -agaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaa -gaagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaaga -agtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggag -gaagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaa -gaagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaa -gaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaag -acaaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttaca -ctctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcc -agagaatc ->p:HG002_1_chr20:13848063-13848750 -atctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggca -gaggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaatt -gcgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaa -gagagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagg -agaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga -agaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaa -gaagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaaga -agtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggag -gaagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaa -gaagaagaggaagaggaagaggaagag---------------gaagaagaagaagaagaa -gaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaag -acaaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttaca -ctctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcc -agagaatc ->p:HG002_2_chr20:13848063-13848750 -atctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggca -gaggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaatt -gcgtctcaaaaaaaaaaaagaa-aagaaaagtagaagacgaagatgaagaagaataagaa -gagagaaaagaagaagagaaggttagagaaaagaagagaaggagaaggagaaggaggagg -agaaggagaaggagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaga -agaagaagaagaagaagaagtcaaatatctggagaagaagaagaagaagaggaagaagaa -gaagaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaaga -agtcaaatatctggagaagaagaagaagaagaggaggaagaagaagaagaagaggaggag -gaagaagaagaagaagaagaagaagaagaagcaggagcaggagaagaagaagaagaagaa -gaagaagaggaagaggaagaggaagaggaagaagaagaagaagaagaagaagaagaagaa -gaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagagaag -acaaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttaca -ctctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcc -agagaatc ->ref_chr20:13848063-13848750 -atctgtaatcccagttattcaggaggctgaggcaggagaatcacctgaacccgggaggca -gaggttccagtgagtcgagatcttgccactgcactccagcctgggggacagagggaaatt -gcgtctcaaaaaaaaaaaagaagaagaaaagtagaagacgaagatgaagaagaataagaa -gagagaaaagaagaagagaaggttagagaaaagaagagaa-------------------- ------gagaaggagaaggagaaggaggaggagaaggagaaggagaagaagaagaagaaga -agaagaagaagaagaagaagtcaaatatctgg---agaagaagaagaagaggaagaagaa -gaaaaggaagaagaagaagaagaggaagaggaagaaagaagaagaacaagaagaagaaga -agtcaaatatctggagaagaagaagaagaagaggaagaagaagaagaagaggaggaggaa -gaaggagaaggagaaggagaaggagaagga------------------------------ -------------------------------------------gaaggagaaggagaagaa -gaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaagaaaat -acaaatatctggagccgggatttgagcctggcccttgacatatgtcctaggcctcttaca -ctctccttaccagcccctgtcccttaggcctgggcccctgatttgcctgtcagagaagcc -agagaatc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a52b319127e719354958ab5fa0bfe32c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a52b319127e719354958ab5fa0bfe32c.msa deleted file mode 100644 index 0360492f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a52b319127e719354958ab5fa0bfe32c.msa +++ /dev/null @@ -1,60 +0,0 @@ ->syndip_1_chr20:62360300-62360712 -tgctgcataggtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatac -gttgggggtgggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtg -ggtgggtggatagggagggggtggggtgggtgcataggtaggggggtggatgggtcagca -ggcagcgggatgggataggataggtgggtgggtggagggatagatgggtggtgggtgggt -ggagggatagatgggtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggat -ggataggtgg--------atgggtgggtggaggaatagatgggtgggtgggtgggtgggt -ggatggataggtgggtgggtgggtggagggatagatgggtgggtgggtgggtggagggat -agatgggtggtgggtgggtggagggatagatgggtggatgggtgggtagaaggataggta ----ggtgggtgggtgggtggatggataggtgggtgggtgggtggaggaata--------g -atgggtgggtggatgggtgggtggagggatagatgggtgggtgggtgggtggagggatag -atgggtgggtgggtggagggaccacttcccaggtggagtggaaagggttcc ->syndip_2_chr20:62360300-62360712 -tgctgcataggtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatac -gttgggggtgggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtg -ggtggagggatagatgggt----------------------------------------- -----------------------ggtgggtgggtggagggataga-------tgggtgggt -ggagggatagatgggtggatgggtgggtagaaggataggtaggtgggtgggtgggtggat -ggataggtgg--------atgggtgggtggaggaatagatgggtgggtgggtgggtgggt -ggatggataggtgggtgggtgggtggaggaataga--------tgggtgggtgga----- -----------tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg ----ggtgggtgggtggaggga--------------------------------------- ------------------------------------------------------------- ----------------------ccacttcccaggtggagtggaaagggttcc ->p:HG002_1_chr20:62360300-62360712 -tgctgcataggtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatac -gttgggggtgggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtg -ggtggagggatgggtg-------------------------------------------- -----------------------agtgggtgggtggagggatagatgggtggtgggtgggt -ggagggatagatgggtgg-tgggtgggtggagggatagatgggtgggtgggtgggtggag -ggatagatggaggaagtggtgggtgggtggagggatagatgggtggatgggtgggtagaa -ggataggtaggtggg----------------------------tgggtgggtgga----- -----------tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg ----ggtgggtgggtggaggga--------------------------------------- ------------------------------------------------------------- ----------------------ccacttcccaggtggagtggaaagggttcc ->p:HG002_2_chr20:62360300-62360712 -tgctgcataggtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatac -gttgggggtgggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtg -ggtggagggatgggtgagtgggtgggtggagggatagatgggtgggtggatgggtcagca -ggcagcgggatgggataggataggtgggtgggtggagggatagatgggtggtgggtgggt -ggagggatagatgggtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggat -ggataggtgg--------atgggtgggtggaggaatagatgggtgggtgggtgggtgggt -ggatggataggtgggtgggtgggtggagggataga--------tgggtgggtggagggat -agatgggtggtgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg -ggtggtgggtgggtggagggatagatgggtggatgggtgggtagaaggataggtaggtgg -gtgggtgggtggatgggtgggtggagggatagatgggtgggtgggtgggtggagggatag -atgggtgggtgggtggagggaccacttcccaggtggagtggaaagggttcc ->ref_chr20:62360300-62360712 -tgctgcataggtaggggggtgggtgggtggatggatgggtaggggtgggtgggtggatac -gttgggggtgggtgggtgggtgggtcagcaggcagagggatgggataggataggtgggtg -ggtggagggatgggtg-------------------------------------------- -----------------------agtgggtgggtggagggatagatgggtggtgggtgggt -ggagggatagatgggtgg-tgggtgggtggagggatagatgggtgggtgggtgggtggag -ggatagatgg-----gtggtgggtgggtggagggatagatgggtggatgggtgggtagaa -ggataggtaggtggg----------------------------tgggtgggtgga----- -----------tgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg ----ggtgggtgggtggaggga--------------------------------------- ------------------------------------------------------------- ----------------------ccacttcccaggtggagtggaaagggttcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a61d80102ac4e0a04abd5fdb28fa4712.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a61d80102ac4e0a04abd5fdb28fa4712.msa deleted file mode 100644 index ddc063f9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a61d80102ac4e0a04abd5fdb28fa4712.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:41196109-41196749 -tagagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccat -tatcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtc -atttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataa -ataaatatataaaaataaatatatatttataataaatatatttttatttcatatataaat -atatatcttataaatatatatatttatataacataaatatatatttatatatattata-- -----------------------aatatatattatatataatatatatttatataaatata -tatattatatataatatatttatatataatatatatttatatattataaatatatattat -atataatatatatttatataaatatatattatatataaatatatattatatataatatat -atttatataaatatatattatatattatataaatattatatataatatatatttatataa -atatatattatatattataaatatatattatatattatatattatataaatattatatat -aatatatattatatataatatatataaaaatatatatatttatatatataaatattttat -caatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgcctt -tttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccc -aaagtgaaggctttgaaggcca ->syndip_2_chr20:41196109-41196749 -tagagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccat -tatcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtc -atttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataa -ataaatatataaaaataaatatatatttataataaatatatttttatttcatatataaat -atatatcttataaatatatatatttatataacataaatatatatttatatatattatata -acataaatatatatttatatatattatatattatatataatatatatttatataaatata -tatattatatataatatatttatatataatatatatttatatattataaatatatattat -atataatatatatttatataaatatatattatatat------------------------ ------tataaatatatattatatattatataaatattatatataatatatatttatataa -atatataatatatattataaatatatattatatattatatattatataaatattatatat -aatatatattatatataatatatataaaaatatatatatttatatatataaatattttat -caatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgcctt -tttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccc -aaagtgaaggctttgaaggcca ->p:HG002_1_chr20:41196109-41196749 -tagagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccat -tatcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtc -atttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataa -ataaatatataaaaataaatatatatttataataaatatatttttatttcatatataaat -atatatcttataaatatatatatttatataacataaatatatatttatatatattatata -acataaatatatatttatatatattatatattatatataatatatatttatataaatata -tatattatatataatatatttatatataatatatatttatatattataaatatatattat -atataatatatatttatataaatatatattatatat------------------------ ------tataaatatatattatatattatataaatattatatataatatatatttatataa -atatataatatatattataaatatatattatatattatatattatataaatattatatat -aatatatattatatataatatatataaaaatatatatatttatatatataaatattttat -caatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgcctt -tttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccc -aaagtgaaggctttgaaggcca ->p:HG002_2_chr20:41196109-41196749 -tagagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccat -tatcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtc -atttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataa -ataaatatataaaaataaatatatatttataataaatatatttttatttcatatataaat -atatatcttataaatatatatatttatataacataaatatatatttatatatattata-- -----------------------aatatatattatatataatatatatttatataaatata -tatattatatataatatatttatatataatatatatttatatattataaatatatattat -atataatatatatttatataaatatatattatatataaatatatattatatataatatat -atttatataaatatatattatatattatataaatattatatataatatatatttatataa -atatatattatatattataaatatatattatatattatatattatataaatattatatat -aatatatattatatataatatatataaaaatatatatatttatatatataaatattttat -caatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgcctt -tttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccc -aaagtgaaggctttgaaggcca ->ref_chr20:41196109-41196749 -tagagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccat -tatcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtc -atttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataa -ataaatatataaaaataaatatatatttataataaatatatttttatttcatatataaat -atatatcttataaatatatatatttatataacataaatatatatttatatat-------- -----------------------attatatattatatataatatatatttatataaatata -tatattatatataatatatttatatataatatatatttatatattataaatatatat--- ------------------------------------------------------------- ------------------------------------------------------------- ---------tatatattataaatatatattatatattatatattatataaatattatatat -aatatatattatatataatatatataaaaatatatatatttatatatataaatattttat -caatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgcctt -tttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccc -aaagtgaaggctttgaaggcca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a647fa2df1390195488545e89b45c36a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a647fa2df1390195488545e89b45c36a.msa deleted file mode 100644 index bc57a35d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a647fa2df1390195488545e89b45c36a.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:57090758-57091276 -acacactccgccatgcacacacacctccacgcacacacacctccacccgcacacacacac -accttcaccaccacacactccacccacacacacctccacccacacacctcca-------- ---------cccacacacacctccgcccacacacacctccgcccacacacacctccaccca -cacacacctccgcccacacacctccgcccacacacacctccgccctcacacacctccacc -cacacacacctccacccacacacgcctccacccgcacacacctccaccaccacacacacc -tccacccacacacaccacccatgcacacacctccacccacacacacacacctccacc--- ----cacacacacctccacccacacgccacccatgcacacacctccacccacacacacaca -caccacccacccacacacacctccacccgcacacacctccaccaccacacacacctccac -ccacacacaccacccatgcacacacctccacccacacacacacacacctccacccacaca -cacctccacccacacaca---ccacccacacacacacacctccacccacacacacacacc -tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc -acacctccactggcacacacca ->syndip_2_chr20:57090758-57091276 -acacactccgccatgcacacacacctccacgcacacacacctccacccgcacacacacac -accttcaccaccacacactccacccacacacacctccacccacacacctccacccacaca -cacctccgcccacacacacctccgcccacacacacctccgcccacacacacctccaccca -cacacacctccgcccacacacctccgcccacacacacctccgccctcacacacctccacc -cacacacacctccacccacacacgcctccacccgcacacacctccaccaccacacacacc -tccacccacacacaccacccatgcacacacctccacccacacacacacacctccacccac -acacacacacacctccacccacacacaccacccacacaca---ccacccatgcacacac- -ctccacccacacacacacacctccacccgcacacacctccaccaccacacacatctccac -ccacacacaccacccatgtgcacacctccactggcacacac------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------ca ->p:HG002_1_chr20:57090758-57091276 -acacactccgccatgcacacacacctccacgcacacacacctccacccgcacacacacac -accttcaccaccacacactccacccacacacacctccacccacacacctccacccacaca -cacctccgcccacacacacctccgcccacacacacctccgcccacacacacctccaccca -cacacacctccgcccacacacctccgcccacacacacctccgccctcacacacctccacc -cacacacacctccacccacacacgcctccacccgcacacacctccaccaccacacacacc -tccacccacacacaccacccatgcacacacctccacccacacacacacacctccacccac -acacacacacacctccacccacacacaccacccacacaca---ccacccatgcacacac- -ctccacccacacacacacacctccacccgcacacacctccaccaccacacacatctccac -ccacacacaccacccatgtgcacacctccactggcacacac------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------ca ->p:HG002_2_chr20:57090758-57091276 -acacactccgccatgcacacacacctccacgcacacacacctccacccgcacacacacac -accttcaccaccacacactccacccacacacacctccacccacacacctccacccacaca -cacctccgcccacacacacctccgcccacacacacctccgcccacacacacctccaccca -cacacacctccgcccacacacctccgcccacacacacctccgccctcacacacctccacc -cacacacacctccacccacacacgcctccacccgcacacacctccaccaccacacacacc -tccacccacacacaccacccatgcacacacctccacccacacacacacacctccacccac -acacacacacacctccacccacacacaccacccacacaca-------------------- ---ccacccacccacacacacctccacccgcacacacctccaccaccacacacacctccac -ccacacacaccacccatgcacacacctccacccacacacacacacacctccacccacaca -cacctccacccacacacacctccacccacatgcacacacctccacccacacacacacacc -tccacccgcacacacctccaccaccacacacatctccacccacacacaccacccatgtgc -acacctccactggcacacacca ->ref_chr20:57090758-57091276 -acacactccgccatgcacacacacctccacgcacacacacctccacccgcacacacacac -accttcaccaccacacactccacccacacacacctccacccacacacctccacccacaca -cacctccgcccacacacacctccgcccacacacacctccgcccacacacacctccaccca -cacacacctccgcccacacacctccgcccacacacacctccgccctcacacacctccacc -cacacacacctccacccacacacgcctccacccgcacacacctccaccaccacacacacc -tccacccacacacaccacccatgcacacacctccacccacacacacacacctccacccac -acacacacacacctccacccacacacaccacccacacaca---ccacccatgcacacac- -ctccacccacacacacacacctccacccgcacacacctccaccaccacacacatctccac -ccacacacaccacccatgtgcacacctccactggcacacac------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------ca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a782fbaa2923dd842acc3a682494c864.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a782fbaa2923dd842acc3a682494c864.msa deleted file mode 100644 index 8f2662f3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a782fbaa2923dd842acc3a682494c864.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:62321286-62321840 -cggtggaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtgg -aagaggtggggccagtgggggtggggtcagtggaggggtggggtcagaggacgggtgggt -tcagaggacgggtgggttcagaggacgggtgggttcagaggacgggtggggtcagtggag -gggtggggtcagtggaggggtagggtcagaggacgggtagggtcagtggaggggtagggc -cagcagaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggagg -ggtggggtcagtggaggcagggtcagtgaaagggtggcgccagtggaggaagagggcgcc -agtggaggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggag -gggtggggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagcc -agtggaagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggag -gcagggccagcagaggggtggggtcagt-----------------ggaggggtggggcca -gtggaggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcaca -caggaaggctagggacagtagaggggtgcagccag ->syndip_2_chr20:62321286-62321840 -cggtggaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtgg -aagaggtggggccagtgggggtggggtcagtggaggggtggggtcagaggac-------- ------------------------------------------------------------- ----------------------------------------------------gggtagggc -cagcagaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggagg -ggtggggtcagtggaggcagggtcagtgaaagggt-------------------ggcgcc -agtggaggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggag -gggtggggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagcc -agtggaagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggag -gcagggccagcagaggggtggggtcagtggaggggtggggccagcggaggggtggggcca -gtggaggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcaca -caggaaggctagggacagtagaggggtgcagccag ->p:HG002_1_chr20:62321286-62321840 -cggtggaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtgg -aagaggtggggccagtgggggtggggtcagtggaggggtggggtcagaggacgggtgggt ------------------------------------------------------------- --------------------------tcagaggacgggtagggtcagtggaggggtagggc -cagcagaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggagg -ggtggggtcagtggaggcagggtcagtgaaagggt------------------------- --------------ggcgccagtggaggaagagggggccagtggaggcagggcctgtggag -gggtggggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagcc -agtggaagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggag -gcagggccagcagaggggtggggtcagt-----------------ggaggggtggggcca -gtggaggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcaca -caggaaggctagggacagtagaggggtgcagccag ->p:HG002_2_chr20:62321286-62321840 -cggtggaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtgg -aagaggtggggccagtgggggtggggtcagtggaggggtggggtcagaggacgggtgggt -tcagaggacgggtgggttcagaggacgggtgggttcagaggacgggtggggtcagtggag -gggtggggtcagtggaggggtagggtcagaggacgggtagggtcagtggaggggtagggc -cagcagaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggagg -ggtggggtcagtggaggcagggtcagtgaaagggtggcgccagtggaggaagagggcgcc -agtggaggaagagggcgccagtggaggaagagggggccagtggaggcagggcctgtggag -gggtggggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagcc -agtggaagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggag -gcagggccagcagaggggtggggtcagt-----------------ggaggggtggggcca -gtggaggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcaca -caggaaggctagggacagtagaggggtgcagccag ->ref_chr20:62321286-62321840 -cggtggaggaagagggggccagtgaaggtgtggggccagtggaggaggtgcagccagtgg -aagaggtggggccagtgggggtggggtcagtggaggggtggggtcagaggacgggtgggt ------------------------------------------------------------- --------------------------tcagaggacgggtagggtcagtggaggggtagggc -cagcagaggggtagggccagcagaggggtggggtcagtggaggggtggggtcagtggagg -ggtggggtcagtggaggcagggtcagtgaaagggt------------------------- --------------ggcgccagtggaggaagagggggccagtggaggcagggcctgtggag -gggtggggccagtggaggtggggtcagtgaaggggtggggccagcggaggaggtgcagcc -agtggaagaggtggggccaatgggggtggggtcagtggaggggtggggtcagtgggggag -gcagggccagcagaggggtggggtcagt-----------------ggaggggtggggcca -gtggaggggtggggtcagtgggggaggaagggccagcagatggggtggggccagggcaca -caggaaggctagggacagtagaggggtgcagccag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a9a3aa630af944b3dea1443420d76716.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a9a3aa630af944b3dea1443420d76716.msa deleted file mode 100644 index 5803bf1d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a9a3aa630af944b3dea1443420d76716.msa +++ /dev/null @@ -1,100 +0,0 @@ ->syndip_1_chr20:278799-279287 -ggatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaa -atgcgtcttccaggtggaggaagcaccacgtgcagt------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gggc -ggggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggag -ggagggcgggagggagggacggagggaggaagggcgggacggagggagggagggcgggag -ggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggag -ggcgggagggcgggacggagggagggag---ggagggagggcgggacggagggagggagg -gagggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgg -agggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggg -agggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgg -agggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagc -agggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctcc -cggttgagcttgctgaggaagttctcacggc ->syndip_2_chr20:278799-279287 -ggatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaa -atgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggc -gcgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggag -ggagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcg -ggacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcg -ggacggagggagggagggagggagggcgggacggagggagggagggcgggacggagggag -ggagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcg -ggacggagggcgggagggcgggacggagggagggagggcgggacggagggacggagggag -ggagggcgggacggagggagggagggcgggacggagggacggagggagggagggcgggac -ggagggagggagggagggacggagggcgggacggcgggagggcgggacggagggacggag -ggagggcgggacggagggcgggagggagggagggcgggacggagggagggagggagggag -ggcgggacggagggagggagggagggagggacggagggacggagggagggagggagggag -ggacggagggcgggacggagggagggagggcggagggagggagggcgggacggagggagg -gagggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgg -agggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggg -agggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgg -agggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagc -agggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctcc -cggttgagcttgctgaggaagttctcacggc ->p:HG002_1_chr20:278799-279287 -ggatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaa -atgcgtcttccaggtggaggaagcaccacgtgcagtgggcggggaaaggcaggagagggc -gcgcgagtgcgcggagggagggcgggacggagggagggagggcgggacggagggagggag -ggagggcgggacggagggagggagggcgggacggagggagggagggagggacggagggcg -ggacggcgggagggcgggacggagggacggagggagggcgggacggagggcgggagggcg -ggacggagggagggagggagggagggcgggacggagggagggagggcgggacggagggag -ggagggagggacggagggcgggacggcgggagggcgggacggagggacggagggagggcg -ggacggagggcgggagggcgggacggagggagggagggcgggacggagggacggagggag -ggagggcgggacggagggagggagggcgggacggagggacggagggagggagggcgggac -ggagggagggagggagggacggagggcgggacggcgggagggcgggacggagggacggag -ggagggcgggacggagggcgggagggagggagggcgggacggagggagggagggagggag -ggcgggacggagggagggagggagggagggacggagggacggagggagggagggagggag -ggacggagggcgggacggagggagggagggcggagggagggagggcgggacggagggagg -gagggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgg -agggagggagggcgggagggatggagggagggagggcgggacggagggagggcgggaggg -agggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgg -agggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagc -agggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctcc -cggttgagcttgctgaggaagttctcacggc ->p:HG002_2_chr20:278799-279287 -ggatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaa -atgcgtcttccaggtggaggaagcaccacgtgcagt------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gggc -ggggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggag -ggagggcgggagggagggacggagggaggaagggcgggacggagggagggagggcgggag -ggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggag -ggcgggagggcgggacggagggagggag---ggagggagggcgggacggagggagggagg -gagggagggacggagggcgggacggagggagggagggcggagggagggagggcgggacgg -agggagggagggcgggacggagggtgggagggagggagggatggaggga----gggaggg -agggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgg -agggacggagggcgggcggatgccgcgggtctcaccgccaaggtgtcctgctgctgcagc -agggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctcc -cggttgagcttgctgaggaagttctcacggc ->ref_chr20:278799-279287 -ggatgaaacccatctcggtcctcttgcaaagcccaggtgaggggagtgaagggtgaagaa -atgcgtcttccaggtggaggaagcaccacgtgcagt------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gggc -ggggaaaggcaggagagggcgcgcgagtgcgcggagggagggcgggacggag----ggag -ggagggcg--------------------------------ggacggagggagggagggag -ggacggagggcgggacggcgggagggcgggacggagggacggagggagggcgggacggag -ggcgggagggcgggacggag---------------------------------------- ------------------------------------------------------------- -------------------------------------------ggaggga----gggaggg -agggacggagggcgggacggagggacggagggagggagggagggacggaggttgggacgg -agggacggagggcgggcggatgccgcgggtctcaccgccagggtgtcctgctgctgcagc -agggcccgcacgtgcagggtcgtgctgttctccatctcctggatggtctcgatcagctcc -cggttgagcttgctgaggaagttctcacggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_a9d398ab39129efb27eabfa2cdf49d07.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_a9d398ab39129efb27eabfa2cdf49d07.msa deleted file mode 100644 index b50a92ee..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_a9d398ab39129efb27eabfa2cdf49d07.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:62349512-62350032 -gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac -aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa -gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg -atgatggtgatggtgggggtgatgatggtgatggtgatggtgatggtgggggtggtgatg -gtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg -acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg -tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg -ggggtgggggtgatgacggtgat---------------------ggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg -atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg -gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg -tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga -tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg -tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag -aggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgggggtga -tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg -tggg-------------------------------------------------------- -ggtgggggtgggggtgatgacggtgat--------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------ggtgggggtgatgatggtgggagtgggctggtagtg -ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg -gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc ->syndip_2_chr20:62349512-62350032 -gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac -aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa -gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg -atgatggtgatggtgggggtgatgatggtgatggtga---------------tggtgatg -gtgatggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg -acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg -tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg -ggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg -atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg -gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg -tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga -tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg -tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag -aggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtga -tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg -tgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatgac -ggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgat -gacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg -ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt -gggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggt -gggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtggg -ggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagtg -ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg -gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc ->p:HG002_1_chr20:62349512-62350032 -gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac -aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa -gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg -atgatggtgatggtgggggtgatgatggtgatggtga---------------tggtgatg -gtgatggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg -acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg -tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg -ggggtgggggtgatgacggtgatggtgggggtgatgacggtgggggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg -atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg -gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg -tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga -tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg -tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag -aggtgatgatggtgggggtgggggtgggggtgggggtgagggtgatgatggtgggggtga -tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg -tgggggtgggggtaatgacggtggggtgggggtaatgacggtgggggtgggggtgatgac -ggtgggggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgat -gacggtgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggg -ggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggt -gggggtgatgacggtgatggtagaggtgatgatggtgggggtgatggtgggggtgggggt -gggggtgggggtgatgatggtgatggtgggggtgatgatggtgagggtgatgatggtggg -ggtgatggtgggggtgggggtgggggtgggggtgatgatggtgggagtgggctggtagtg -ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg -gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc ->p:HG002_2_chr20:62349512-62350032 -gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac -aattccggatagactgtcatggaatagaaaaactacagggtgcatttcaggaaggaggaa -gcagcaacccaggggatggggatggggatggggatggggatggtgggggtgatgggggtg -atgatggtgatggtgggggtgatgatggtgatggtgatggtgatggtgggggtggtgatg -gtgggggtgggggtggtgatggtgggggtgggggtgatgatggtgatggtgggggtgatg -acggtggggctgggggtgatgatggtgggggtgatgacggtgatgatgggggtggagggg -tgatgacggtgatgatgggggtgggggggtgatgacggtgatgtgggggtgatgacggtg -ggggtgggggtgatgacggtgat---------------------ggtgggggtgatgacg -gtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatg -acggtgggggtgggggtgatgatggtgatggtgggggtgatgatggtgggggtgggggtg -atgatggtgagggtgatgatggtgggggtaatgacggtggggtgggggtgatgacggtgg -gggtgggggtgatgacggtgatggtgggggtgatgacgatgatggtgggggtgatgacgg -tgatggcggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtgggggtga -tgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgggggtggggg -tgatgacggtgggggtgggggtgatgacggtgggggtgggggtgatgacggtgatggtag -aggtgatgatggtgggggtgatggtgggggtgggggtggg---------ggtgggggtga -tgatggtgatggtgggggtgatgatggtgagggtgatgatggtgggggtgatggtggggg -tggg-------------------------------------------------------- -ggtgggggtgggggtgatgacggtgat--------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------ggtgggggtgatgatggtgggagtgggctggtagtg -ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg -gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc ->ref_chr20:62349512-62350032 -gaatcctacagtcagctcaactatcattcaagagggaggacaaaacagccgttttcagac -aattccggatagactgtcatggaatagaaaaactacagggtgcatttcag---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------gaaggaggaag -cagcaacccaggggatggggatggggatggggatggtgggggtgatgggggtgatgatgg -tgatggtgatggtgatggtgatggtgatggtgatggtggg---------ggtggtgatg- -----------ggtgggggtgatgacggtgggagtgggggtgatgacggtgatggtggggg -tgat-----------------------------------------------------gac -ggtgatggtgggggtgatgacggtgat--------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------ggtgggggtgatgatggtgggagtgggctggtagtg -ggggtgatggtttgggtgggagtaaggtgatggtggaggtaaagaggcagaaaattgctg -gctgatgacatggagcccccttccctggaggagaggtggggtggcgggtaaagggtgcag -ggagaacatgggcaggctaatgttttgggacactggtgggtgaccaggtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_aa3a05349bc510949f2591f228f1864a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_aa3a05349bc510949f2591f228f1864a.msa deleted file mode 100644 index 96282c01..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_aa3a05349bc510949f2591f228f1864a.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:5041831-5042378 -atgtcctaaaaaccctttttcaagagtctctccccagctgctgctagcgggatttttttt -ttaactctctatcctatttaacctcctcactgatgaccttttaatgcgtaac-------- ---------------------ttttttttttttttttttttttgagacggagtctcgctct -cccaggctggagtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttca -agcgatctcctgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcata -gctaatgtttgtatttttagtagagacggggtttcaccatgttggccaggctggttatgc -ataactttttatcacagatgtttgatctcagttttaatcttttcaacatttgtaaaccct -tggttcattgtgcttctccctttattactc------------ttttttttttttttttga -gacggagtttcgctcttgttgcccaggctggagtgcagtggcgcactctcggttcactgc -aatctccacctcataggttcaagcgattctcctgcc------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------- ->syndip_2_chr20:5041831-5042378 -atgtcctaaaaaccctttttcaagagtctctccccagctgctgctagcgggatttttttt -ttaactctctatcctatttaacctcctcactgatgaccttttaatgcgtaactttttttt -ttttttttttttttttttttttttttttttttttttttttttgagacggagtctcgctct -cccaggctggagtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttca -agcgatctcctgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcata -gctaatgtttgtatttttagtagagacggggtttcaccatgttggccaggctggttatgc -ataactttttatcacagatgtttgatctcagttttaatcttttcaacatttgtaaaccct -tggttcattgtgcttctccctttattactcttttttttttttttttttttttttttttga -gacggagtttcgctcttgttgcccaggctggagtgcagtggcgcactctcggttcactgc -aatctccacctcataggttcaagcgattctcctgcc------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------- ->p:HG002_1_chr20:5041831-5042378 -atgtcctaaaaaccctttttcaagagtctctccccagctgctgctagcgggatttttttt -ttaactctctatcctatttaacctcctcactgatgaccttttaatgcgtaactttttttt -ttttttttttttttttttttttttttttttttttttttttttgagacggagtctcgctct -cccaggctggagtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttca -agcgatctcctgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcata -gctaatgtttgtatttttagtagagacggggtttcaccatgttggccaggctggttatgc -ataactttttatcacagatgtttgatctcagttttaatcttttcaacatttgtaaaccct -tggttcattgtgcttctccctttattactcttttttttttttttttttttttttttttga -gacggagtttcgctcttgttgcccaggctggagtgcagtggcgcactctcggttcactgc -aatctccacctcataggttcaagcgattctcctgcc------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------- ->p:HG002_2_chr20:5041831-5042378 -atgtcctaaaaaccctttttcaagagtctctccccagctgctgctagcgggatttttttt -ttaactctctatcctatttaacctcctcactgatgaccttttaatgcgtaac-------- ---------------------ttttttttttttttttttttttgagacggagtctcgctct -cccaggctggagtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttca -agcgatctcctgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcata -gctaatgtttgtatttttagtagagacggggtttcaccatgttggccaggctggttatgc -ataactttttatcacagatgtttgatctcagttttaatcttttcaacatttgtaaaccct -tggttcattgtgcttctccctttattactc------------ttttttttttttttttga -gacggagtttcgctcttgttgcccaggctggagtgcagtggagcactctcggttcactgc -aacctccacctcataggttcaagcgattctcctgcctcagcctcctgagtagctgggatt -acaggtgcccaccaccatgcccttttttttttttgagacggagtttcgctcttgttgccc -aggctggagtgcagtggcgcactctcggttcactgcaatctccacctcataggttcaagc -gattctcctgcc ->ref_chr20:5041831-5042378 -atgtcctaaaaaccctttttcaagagtctctccccagctgctgctagcgggatttttttt -ttaactctctatcctatttaacctcctcactgatgaccttttaatgcgtaac-------- ---------------------ttttttttttttttttttttttgagacggagtctcgctct -cccaggctggagtgcagtggtgtgatctcggctcactgcaacctgtgcctcccaggttca -agcgatctcctgcctcagcctccccagtacctaggattacaggtgcgcgcctccagcata -gctaatgtttgtatttttagtagagacggggtttcaccatgttggccaggctggttatgc -ataactttttatcacagatgtttgatctcagttttaatcttttcaacatttgtaaaccct -tggttcattgtgcttctccctttattactcttttttttttttttttttttttttttttga -gacggagtttcgctcttgttgcccaggctggagtgcagtggcgcactctcggttcactgc -aatctccacctcataggttcaagcgattctcctgcc------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_aaf3284dfcd9e22479f7e2d5c0551083.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_aaf3284dfcd9e22479f7e2d5c0551083.msa deleted file mode 100644 index b9a35234..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_aaf3284dfcd9e22479f7e2d5c0551083.msa +++ /dev/null @@ -1,240 +0,0 @@ ->syndip_1_chr20:22081861-22084222 -ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg -tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc -gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt -attaatatatattaatataatataataataatacaatataatatatgtatatatgtaggt -atataataatatacctacatatatacatatattatatatactatctgtatattatatgta -taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt -atatattataagtatatactatacatgcatgtattatatgtatatac------------- ----------------tatacatgcatgtattatatgtatatattatacatgcatgtatta -tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg -tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat -attaaacacgtttatattatttattatacatgactatattatataggtatatatgatata -tgcatatatgtcatataggtatatatgacatatatgcatatatcatgtaggtatatatga -catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatat -atgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggt -atatatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatat -aggtatatatgatatatgcgcatatatcatacaggtatatgtgcatatatcatataggta -taggtataggtagatatatgatatatgcacacatatcatataggtatatatgatatatga -taggtatatatgatatatgataggtatatatgatatatatcatattggtatatatgatat -atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt -atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata -tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat -attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat -atatatgtatatatattatataggtatatataatatatgtgtatatattatgtgggtata -tataatatatgtgtacatattatgtgggtatatataatatatgtgtacatattatgtggg -tatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatg -tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatat -tatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat -atattatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgt -gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat -atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat -aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag -aaatattatatatacg---------------------------------tatattaatat -agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata -ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta -tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg -tatatattatgtatgtatatattatatatacgtatatattaatatgcatatatatgtgtc -tctttataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta -ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc -atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata -cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca -tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctc ->syndip_2_chr20:22081861-22084222 -ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg -tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc -gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt -attactatatattaatataatataataataatacaatataatatatgtatatatgtaggt -atataataatatacctacatatatacatatattatatatactatctgtatattatatgta -taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt -atatattataagtatatactatacatgcatgtattatatgtatatac------------- ----------------tatacatgcatgtattatatgtatatattatacatgcatgtatta -tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg -tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat -attaaacacgtttatattatttattata-------------------------------- --------------------------------------------catgtaggtatatatga -catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacagg----- -----tatatgcgcatatatcatataggtataggt------------------ataggtag -atatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatat -aggtatatatgatatatg------------------------------------------ ----------------------------------------ataggtatatatgatatatga -ta--------------------------------------------ggtatatatgatat -atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt -atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata -tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat -attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat -atatatgtgtatatattatata-------------------------------------- ------------------------------------------------------------- -------------------------------ggtatatataatatatgtgtatatattatg -tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatat -tatgtgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat -atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt -gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat -atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat -aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag -aaatattatatatacgtatattaatatagacgtatatataatatatacatatattaatat -agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata -ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta -tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg -tatatattatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtc -tcattataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta -ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc ------------------------------------------------------------- -------------------------------atatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata -cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca -tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctc ->p:HG002_1_chr20:22081861-22084222 -ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg -tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc -gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt -attactatatattaatataatataataataatacaatataatatatgtatatatgtaggt -atataataatatacctacatatatacatatattatatatactatctgtatattatatgta -taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt -atatattataagtatatactatacatgcatgtattatatgtatatac------------- ----------------tatacatgcatgtattatatgtatatattatacatgcatgtatta -tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg -tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat -attaaacacgtttatattatttattata-------------------------------- --------------------------------------------catgtaggtatatatga -catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacagg----- -----tatatgcgcatatatcatataggtataggt------------------ataggtag -atatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatat -aggtatatatgatatatg------------------------------------------ ----------------------------------------ataggtatatatgatatatga -ta--------------------------------------------ggtatatatgatat -atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt -atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata -tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat -attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat -atatatgtgtatatattatata-------------------------------------- ------------------------------------------------------------- -------------------------------ggtatatataatatatgtgtatatattatg -tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatat -tatgtgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat -atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt -gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat -atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat -aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag -aaatattatatatacgtatattaatatagacgtatatataatatatacatatattaatat -agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata -ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta -tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg -tatatattatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtc -tcattataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta -ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc ------------------------------------------------------------- -------------------------------atatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata -cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca -tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctc ->p:HG002_2_chr20:22081861-22084222 -ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg -tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc -gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt -attaatatatattaatataatataataataatacaatataatatatgtatatatgtaggt -atataataatatacctacatatatacatatattatatatactatctgtatattatatgta -taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt -atatattataagtatatactatacatgcatgtattatatgtatatac------------- ----------------tatacatgcatgtattatatgtatatattatacatgcatgtatta -tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg -tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat -attaaacacgtttatattatttattatacatgactatattatataggtatatatgatata -tgcatatatgtcatataggtatatatgacatatatgcatatatcatgtaggtatatatga -catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggtatat -atgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatataggt -atatatgatatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatat -aggtatatatgatatatgcgcatatatcatacaggtatatgtgcatatatcatataggta -taggtataggtagatatatgatatatgcacacatatcatataggtatatatgatatatga -taggtatatatgatatatgataggtatatatgatatatatcatattggtatatatgatat -atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt -atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata -tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat -attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat -atatatgtatatatattatataggtatatataatatatgtgtatatattatgtgggtata -tataatatatgtgtacatattatgtgggtatatataatatatgtgtacatattatgtggg -tatatataatatatgtgtacatattatgtgggtatatataatatatgtgtatatattatg -tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtatatat -tatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtat -atattatgtgggtatatataatatatgtgtatatattatgtgggtatatataatatatgt -gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat -atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat -aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag -aaatattatatatacg---------------------------------tatattaatat -agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata -ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta -tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg -tatatattatgtatgtatatattatatatacgtatatattaatatgcatatatatgtgtc -tctttataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta -ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc -atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata -cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca -tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctc ->ref_chr20:22081861-22084222 -ggatggttccatatttttgcagttgtgtattttgctgctataaacatgtgtgtgcaggtg -tctttttcatataacaacttcttttcctttgggtaggtttacaaaaactatctttttccc -gttcttttacttatatatgcttatttatatatattatatatacacttttaatatatactt -attactatatattaatataatataataataatacaatataatatatgtatatatgtaggt -atataataatatacctacatatatacatatattatatatactatctgtatattatatgta -taatatatgtatatataatatatgtatatactatacatgtatatattatattatacatgt -atatattataagtatatactatacatgcatgtattatatgtatatactatacatgcatgt -attatatgtatatattatacatgcatgtattatatgtatatattatacatgcatgtatta -tatgtatatattatacatgcatgtattatatgtatatattatacatgtatgtattatatg -tatagattatacatgtatatattatatatgtatatattacacatgtacatatatgtatat -attaaacacgtttatattatttattata-------------------------------- --------------------------------------------catgtaggtatatatga -catatgcatatatcatataggtatatatgacatatgcatatatcatataggtatatatga -tatatgcgcatatatcatataggtatatatgatatatgcgcatatatcatacagg----- -----tatatgcgcatatatcatataggtataggt------------------ataggtag -atatatgatatatgcacacatatcatataggtatatatgatatatgcgcatatatcatat -aggtatatatgatatatg------------------------------------------ ----------------------------------------ataggtatatatgatatatga -ta--------------------------------------------ggtatatatgatat -atatcatatcggtatatatgatatatatcatatcggtatatataggtatatatcataggt -atatataggtatatatcacataggtatatataggtatatatcatataggtatatataata -tatgcatttatattatataggtatatatattacataggtatatgtaatatgtgcatatat -attatataggtatatatattatacaggcatatataatacgtatatatattatatgggcat -atatatgtgtatatattatata-------------------------------------- ------------------------------------------------------------- -------------------------------ggtatatataatatatgtgtatatattatg -tgggtatatataatatatgtgtatatattatgtgggtatatataatatatgtgtacatat -tatgtgggtatatataatatatgtgtatatattatgtaggtatatataatatatgtgtat -atattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatatatgt -gtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatataatat -atgtgtatatattatgtaggtatatataatatatgtgtatatattatgtaggtatatata -atatatgtgtatatattatgtaggtatatataatatatgtgtatatattatatatgtaat -aggaagcaggaatgaatgcacagaagaccttagagtttaaggcattatttgtgtaatgag -aaatattatatatacgtatattaatatagacgtatatataatatatacatatattaatat -agacgtatatataatatatacatatatacatatatagtatatactatgtatacatatata -ctatacatacgtatattatatacatgtgtattatatacatgtgtattatatatatgtgta -tacatatatactatatatacatacattatatacatacattatatatgtgtattatatatg -tatatattatgtatgtatatattatatatacgtatatattaatatacatatatatgtgtc -tcattataccaataatgccttaaactctaaggtcttctgtgcattcattcctgcttccta -ttacatatatattatatagatacatatataatatatacatatatactacataatatatgc ------------------------------------------------------------- -------------------------------atatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtatatataatatatacatatgttgtatatgt -atatataatatatacatatgttgtatatgtattatatgtatatattacatattatatata -cttatgtatgtataatatatatataatatatatatatcttaggcaacttttcattgctca -tttttattaaaccctgaaaactttcactttactccatttctaagtttgatattctggtag -aattaaagtaagagttttctttctttcatctcctttttatctctctc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ac49004ec0dccaa0aa222eebaca554b5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ac49004ec0dccaa0aa222eebaca554b5.msa deleted file mode 100644 index 360afd32..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ac49004ec0dccaa0aa222eebaca554b5.msa +++ /dev/null @@ -1,170 +0,0 @@ ->syndip_1_chr20:8661811-8662757 -gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa -gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc -tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta -tataattatttattatataattatatataattatataattatttattatataattatata -taa-tatacaattatttattatataattatatataattatatatttattatatttat--- ---tatacagttatataataaataattatataattatatataattatata---------ta -tataattatatataattatata-----taattatataattatatataattg--------- -----------------------tatataattatttattatataattatat---------- --attatttattatataattatata----------------attatat------------- ------attatttattatata---------------------------------------- ---------------------ttatataattatataattatatattatttattatata--- ---atatataattatatat-------tatttattatataattatatattatttatta---- ------tatatattatttattatata----------------------attatatattatg -tattatataattatataattatatattatgtattatataat----------------tat -atattatgtattatataattatataattatatattatgtattatataattatatattatt -tattatataattatataattatatattatttattatataattatataattatatattatt -tattatataat---------------------tatataattatatattatttattatata -attatataattatat-attattt--------attatataattatatattatttattatat -aattatatattatttattacataaatatatattatttattacataagtatatatcactta -ttatataattgcatataattatttattatataattgcatataa----ttattatataatt -gtatatagttatttattatataattgtatatagttatttattatataattctatataatt -atttattatctaattctatattaaatataattatttattatc------------------ ---------------taattctatattatatataattatttattatataattctatattat -atataattattatataattctatatataattatttattatataattctatacataagtat -ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt -tattatataattatgtataatatgtaattatttattatataattatgtataatatataat -tatttattatataattatgtataatatataattatttattatataattatgtgttatgta -taa----ttattatataattatgtataatatatatataattttttattatataattatgt -ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat -atatattattaacataatatctaaatatattaataatctaatatctataattaatataat -atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa -tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacac ->syndip_2_chr20:8661811-8662757 -gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa -gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc -tcttaaaagtgtatatatatataattatataattatttattatataatgatatataatta -tataattatttattatataatgatatataattatataattatttattatataattatata -taattatataattatttattatataattatatataattatataattatttattatataat -tatatataattatataattatttattatataattatatataattatataattatttatta -tataattatatataattatataattatttattatataattatatataattatataattat -ttattatataattatatataattatataattatttattatataattatatataattatat -aattatttattatataattatatataatatacaattatttattatataattatatataat -atacaattatttattatataattatatataattatatatttattatatttattatacagt -tatataataaatatataattatatataaatatataattatatataattatatatatataa -ttatatgtaattatatataattatataattattatataattgtatataatatataattat -ataattatatattatttattatataatatataattatataattatatattatttattata -taatatataattatataattatatattatttattatataattatatattatttattatat -atattatttattatataattatataattatatattatttattatataattatatattatt -tattatataa-tatataattatatattatttattatataa-tatataattatatattatt -tattatataattatatattatgtattatataatatataattatatattatgtattatata -attatataattatat-attatttattatataattatataattatatattatttattacat -aattatatattatttattacataagtatatattatttattacataagtatatatcactta -ttatataattgtatataattatttattatataattgcatataattatttattatataatt -gtatatagttatttattatataattctatatagttatttattatataattctatataatt -atttattatctaattctatattatatataattatttattatctaattctatattatatat -aattatttattatataattctatattatatataattatttattatataattctatattat -atataattattatataattctatatataattatttattatataattctatacataagtat -ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt -tattatataattatgtataatatataattgtttattatataattatgtataatatataat -tatttattatataattatgtataatatataattatttattatataattatgtgttatgta -taattatttattatataattatgtataatatatatataattttttattatataattatgt -ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat -atatattattaacataatatctaaatatattaataatctaatatctataattaatataat -atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa -tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacac ->p:HG002_1_chr20:8661811-8662757 -gccaacctacgttaagtaattcataacttcagtattcaataaatcttcagtgaaaggcaa -gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc -tcttaaaagtgtatatatatataattatataattatttattatataatgatatataatta -tataattatttattatataatgatatataattatataattatttattatataattatata -taattatataattatttattatataattatatataattatataattatttattatataat -tatatataattatataattatttattatataattatatataattatataattatttatta -tataattatatataattatataattatttattatataattatatataattatataattat -ttattatataattatatataattatataattatttattatataattatatataattatat -aattatttattatataattatatataatatacaattatttattatataattatatataat -atacaattatttattatataattatatataattatatatttattatatttattatacagt -tatataataaatatataattatatataaatatataattatatataattatatatatataa -ttatatgtaattatatataattatataattattatataattgtatataatatataattat -ataattatatattatttattatataatatataattatataattatatattatttattata -taatatataattatataattatatattatttattatataattatatattatttattatat -atattatttattatataattatataattatatattatttattatataattatatattatt -tattatataa-tatataattatatattatttattatataa-tatataattatatattatt -tattatataattatatattatgtattatataatatataattatatattatgtattatata -attatataattatat-attatttattatataattatataattatatattatttattacat -aattatatattatttattacataagtatatattatttattacataagtatatatcactta -ttatataattgtatataattatttattatataattgcatataattatttattatataatt -gtatatagttatttattatataattctatatagttatttattatataattctatataatt -atttattatctaattctatattatatataattatttattatctaattctatattatatat -aattatttattatataattctatattatatataattatttattatataattctatattat -atataattattatataattctatatataattatttattatataattctatacataagtat -ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt -tattatataattatgtataatatataattgtttattatataattatgtataatatataat -tatttattatataattatgtataatatataattatttattatataattatgtgttatgta -taattatttattatataattatgtataatatatatataattttttattatataattatgt -ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat -atatattattaacataatatctaaatatattaataatctaatatctataattaatataat -atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa -tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacac ->p:HG002_2_chr20:8661811-8662757 -gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa -gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc -tcttaaaagtgtatatatatataattatataattatttattatataattatatataatta -tataattatttattatataattatatataattatataattatttattatataattatata -taa-tatacaattatttattatataattatatataattatatatttattatatttat--- ---tatacagttatataataaataattatataattatatataattatata---------ta -tataattatatataattatata-----taattatataattatatataattg--------- -----------------------tatataattatttattatataattatat---------- --attatttattatataattatata----------------attatat------------- ------attatttattatata---------------------------------------- ---------------------ttatataattatataattatatattatttattatata--- ---atatataattatatat-------tatttattatataattatatattatttatta---- ------tatatattatttattatata----------------------attatatattatg -tattatataattatataattatatattatgtattatataat----------------tat -atattatgtattatataattatataattatatattatgtattatataattatatattatt -tattatataattatataattatatattatttattatataattatataattatatattatt -tattatataat---------------------tatataattatatattatttattatata -attatataattatat-attattt--------attatataattatatattatttattatat -aattatatattatttattacataaatatatattatttattacataagtatatatcactta -ttatataattgcatataattatttattatataattgcatataa----ttattatataatt -gtatatagttatttattatataattgtatatagttatttattatataattctatataatt -atttattatctaattctatattaaatataattatttattatc------------------ ---------------taattctatattatatataattatttattatataattctatattat -atataattattatataattctatatataattatttattatataattctatacataagtat -ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt -tattatataattatgtataatatgtaattatttattatataattatgtataatatataat -tatttattatataattatgtataatatataattatttattatataattatgtgttatgta -taa----ttattatataattatgtataatatatatataattttttattatataattatgt -ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat -atatattattaacataatatctaaatatattaataatctaatatctataattaatataat -atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa -tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacac ->ref_chr20:8661811-8662757 -gccaacctacgttaagtaattcataacttcagtatttaataaatcttcagtgaaaggcaa -gaggctacacacagtgacagacccagagataaaccctgtgcccctagagatttgcactcc -tcttaaaag--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------------tgtata -tatatataattatataattattt--------attatataattatatataattatata--- ---------attatttattatataattatatataatatac------------aattattta -ttatataattatatataattatat--------atttattatat----ttattatacagt- --tatataataaataattatataattatatataattatat------------------att -atttattatctaattctatattaaatataattatttattatc------------------ ---------------taattctatattatatataattatttattatataattctatattat -atataattattatataattctatatataattatttattatataattctatacataagtat -ttattatataattatgtatataattatttattatataattatgtataatatgtaattatt -tattatataattatgtataatatgtaattatttattatataattatgtataatatataat -tatttattatataattatgtataatatataattatttattatataattatgtgttatgta -taa----ttattatataattatgtataatatatatataattttttattatataattatgt -ataatatataattttttataattatgtgtaatatataattatttatcatataattacaat -atatattattaacataatatctaaatatattaataatctaatatctataattaatataat -atataaatattacttcttgaaatccaacgtgcacctgaatcacctgagccgttgttaaaa -tgcagattcgagatcctgcatttctaacaagttactgggtgaggcagaagatgcttagca -aaggcccacac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_acc5b39b9b4e309d6651a395ca73d3b6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_acc5b39b9b4e309d6651a395ca73d3b6.msa deleted file mode 100644 index 8f475c41..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_acc5b39b9b4e309d6651a395ca73d3b6.msa +++ /dev/null @@ -1,60 +0,0 @@ ->syndip_1_chr20:62270303-62270937 -cctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtc -ctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctccttgtc -cctctctgg-----------------------------gtcctctccttgtccctctctg -ggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtc ->syndip_2_chr20:62270303-62270937 -cctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtc -ctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctga-------------------------------------------cctctctg -ggtcctctccttgtccctctctgggtcctctccttgtc---------------------- --------------------cctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtc--------------------------------------------------- ------------------------------------- ->p:HG002_1_chr20:62270303-62270937 -cctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtc -ctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctgg-------------------------------------------cctctctg -ggtcctctc-----------------------------------------ctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtc--------------------------------------------------- ------------------------------------- ->p:HG002_2_chr20:62270303-62270937 -cctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtc -ctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctgg-----------------------------gtcctctccttgtccctctctg -ggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtc ->ref_chr20:62270303-62270937 -cctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctgggtc -ctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctctctg -ggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctccttgtc -cctctctggcctctctgggtcctctctgacctctctgggtcctctccttgtccctctctg -ggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcc -tctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcc -ttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtcct -ctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctccttgtc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae89171a433f770e25870ba2623263b5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ae89171a433f770e25870ba2623263b5.msa deleted file mode 100644 index 15777a46..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ae89171a433f770e25870ba2623263b5.msa +++ /dev/null @@ -1,130 +0,0 @@ ->syndip_1_chr20:48449605-48450561 -catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg -tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa -taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg -gatggatggggtgggatgggatgggatg-----ggatggatggatgggatggatggatgg -gatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggatg -ggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaat -gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga -tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat -gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg -ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat -ggat-----------------------ggatgggatgggatggatggatgggatgggatg -ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg -atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg -gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg -atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag -atgggatggatggcatgggatgggatgggattggatggggtgggatgggatggggtagga -tgggatgggatgggatgggatgggatgggatgggatgggatgggatggggtgggatgggt -tgggatgggatggggtgggttgggatggggtggggtgggatgggatgggatgggatgggg -tggggtggggtggggtgggatggggtgggatggggtgggatgggatggggtgggatggga -tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga -tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga -ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg -ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa -atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacag ->syndip_2_chr20:48449605-48450561 -catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg -tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa -taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg -gatggatggggtgggatgggatgggatg-------------ggatggggtggatggatgg -gatgggataggatggatggggtgagatgggatggaatggatggaatgggatggatggatg -ggatgggatggatgggatgggatggatgggatggatgggatgggatggatgggatggaat -gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga -tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat -gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg -ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat -ggatggatgggatgggatggatggatgggatgggatgggatggatggatgggatgggatg -ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg -atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg -gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg -atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag -atgggatggatggcatgggatggaatgggattggatggggtgggatgggatggggtagga -tgggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatgggg -tgggttgggatgggg----------tggggtgggatgggatgggatggggtgggatgggg -tgggatggggtgggatggggtgggatgggatggggtgggatgggatgggatgggatgggg -tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga -tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga -ttggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggtg -ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa -atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacag ->p:HG002_1_chr20:48449605-48450561 -catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg -tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa -taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg -gatggatggggtgggatgggatgggatg-------------ggatggggtggatggatgg -gatgggataggatggatggggtgagatgggatggaatggatggaatgggatggatggatg -ggatgggatggatgggatgggatggatgggatggatgggatgggatggatgggatggaat -gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga -tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat -gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg -ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat -ggatggatgggatgggatggatggatgggatgggatgggatggatggatgggatgggatg -ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg -atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg -gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg -atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag -atgggatggatggcatgggatggaatgggattggatggggtgggatgggatggggtagga -tgggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatgggg -tgggttgggatgggg----------tggggtgggatgggatgggatggggtgggatgggg -tgggatggggtgggatggggtgggatgggatggggtgggatgggatgggatgggatgggg -tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga -tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga -ttggatggggtgggatgcgatgggatgagatgagatgagatgaatggcatgggatgggtg -ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa -atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacag ->p:HG002_2_chr20:48449605-48450561 -catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg -tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa -taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg -gatggatggggtgggatgggatgggatg-----ggatggatggatgggatggatggatgg -gatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggatg -ggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaat -gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga -tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat -gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg -ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat -ggat-----------------------ggatgggatgggatggatggatgggatgggatg -ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatggaatgg -atgaatgggatgtgatggatgggatggaatgggatagatgggatgggattggatgggatg -gggtgggatggggtaagatggggtgggatgggatggtatgggatggatggatgagatggg -atgggatgagatgggattggatggggtgggatgcaatgggatgagatgagatgagatgag -atgggatggatggcatgggatgggatgggattggatggggtgggatgggatggggtagga -tgggatgggatgggatgggatgggatgggatgggatgggatgggatggggtgggatgggt -tgggatgggatggggtgggttgggatggggtggggtgggatgggatgggatgggatgggg -tggggtggggtggggtgggatggggtgggatggggtgggatgggatggggtgggatggga -tgggatggggtgggatgggatggggtggggtggggtggggtgggatgaggtggggtggga -tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga -ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg -ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa -atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacag ->ref_chr20:48449605-48450561 -catgagaatatgctcagtgataaggcagtggcgttaaatctgcaggcagtgggctatctg -tgggtccttaaatctatttagtgcatcttgaacagtatttttaagctgggataagtggaa -taggaaggagtggagtggagcatgatggtatgggatgggatggatgggatgggatggatg -gatggatggggtgggatgggatgggatgggatgggatggatggatgggatggatggatgg -gatgggataggatggatggggtgagatgggatggaatggatgggatgggatggatggatg -ggatgggatggatgggatgggatggatgggatgggatggatgggatggatgggatggaat -gggatggatgggatgggatgggattggatggggtgggatgggatggatggatgggatgga -tggatgggatggaatggatggatgggatgggatggatgggatgggatggatggatgggat -gggatggatgcaatggatggatgggatgggatgggatgggatggatggaatggatggatg -ggatgggatgggatggatggggtgggatgagatggatgggatggatgggatgggatggat -ggat-----------------------ggatgggatgggatggatggatgggatgggatg -ggatggggtggatgggatggatggatggatgggatgggatggatggatgggatgggat-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------gga -tgggatgggatggggtggggtggggtgggatgggatgggatggggtggggtgggatggga -ttggatggggtgggatgcgatgg-----gatgagatgagatggatggcatgggatgggtg -ggaggggatgggatattatcagatggcaaaagtaagaagtgttcatattttgtcttcaaa -atataaatatgagtgcataatggcttgtgatgcaaaatacatttcttactaaagatcatg -gacaaagcacttaaaaccacacag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b05e3a291363048d6af177602ce2b043.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b05e3a291363048d6af177602ce2b043.msa deleted file mode 100644 index 40bd6c04..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b05e3a291363048d6af177602ce2b043.msa +++ /dev/null @@ -1,155 +0,0 @@ ->syndip_1_chr20:14861837-14862841 -gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt -attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac -attggaggttttatatataaatatatatatatatttatatatatatttatatatatatat -atttatatatatttatatatatatttatatatatatttatatatatatttatatatatat -ttatatatatatttatatatatatttatatatatatttatatatatatttatatatattt -atatatatttatatatatttttatatatttttatatatataaatatataaaaatatatat -aaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaat -atatataaatatatatttatatataaatatatataaatatatatttatacataaatatat -ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat -acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa -tatatatttatacataaatatataaatatatatataaatatatataaatatatataaata -tatatataaatatatatataaatatatataaatatatatataaatatatatataaatata -tataaatatatataaatatatatataaatatatataaatatatataaatatatatttata -tattaatatataaatatatataaatatatatttatatattaatatataaatatatatata -ttaatatatataaatatatataaatatatatttatatattaatatatatatattaatata -tatatatttatatattaatatatatatttatatattaatatatataaatatattactatg -tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata -tatattaatatataaaatatatatataaatataaataaatatatatataaatatatataa -ataaatatatatataaatatatataaataaatatataaatatatataaatatatatataa -atatatataaatatatataaatatatataaaaatatatataaatatatatataaatatat -ataaatatatatataaatatatatataaatatatatataaatatatataaatatatatat -aaatatatataaatatatatataattatatataaatatatataaatatatataaatatat -atataaatatatataaatatatataaatatatataaatatatatataaatatatataaat -atatatatataaatatatataaatatatatataaatatatataaatatatatatataaat -atatataaatatatatataaatatatataaatatatatataaatataaatatatatgtat -aaatatatatataaatataaatatatatgtataaatatatatataaatatatatatataa -atatatatatacatatataaatatatatataaatatatataaaaatatatatatatatat -ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct -tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaa ->syndip_2_chr20:14861837-14862841 -gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt -attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac -attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat -atttatatatatt----------------------------------------------- ----------------tatatatatttatatatatatttttatatatatttatatatatt- --tatatatttatatatatttatatatatttttatatatataaatatataaaa-------- ------------------------------------------------------------- -----------------------------atatataaatatatataaatatataaatatat -ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat -acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa -tatatatttatacataaatatataaatatat------atatatataaatatatataa--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------atatatatttatatattaatatatataaatatattactatg -tatatttatatatatttatataa--atatataaatatatgtaaatatatatataaaaata -tatattaatatataaaa---------atatatatataaatatatatataaatatatataa -ataaatatatataaatatatatataaat--atatataaatatatataaatatatatataa -atatatataaatatatataaatatatatataaatatatatataaatatatataaatatat -ataaataaatatataaatatatatataaatatatataaatatatatataaatatatataa -atatatatataaatatatataaatatatatataaatatatataaat--------atatat -ataaatatatatataaatatatataaatatatataaatatatatatataaatatatataa -atatatatataaatataaatatatataaatatataaaaatatatatataaatataaatat -atataaatatatatgtataaatatatatataaatataaatatatataaatatatatatat -aaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaat -atatatataaatatatataaatatatatataaatatatataaaaatatatatatattttt -ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct -tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaa ->p:HG002_1_chr20:14861837-14862841 -gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt -attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac -attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat -atttatatatatt----------------------------------------------- ----------------tatatatatttatatatatatttttatatatatttatatatatt- --tatatatttatatatatttatatatatttttatatatataaatatataaaa-------- ------------------------------------------------------------- -----------------------------atatataaatatatataaatatataaatatat -ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat -acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa -tatatatttatacataaatatataaatatat------atatatataaatatatataa--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------atatatatttatatattaatatatataaatatattactatg -tatatttatatatatttatataa--atatataaatatatgtaaatatatatataaaaata -tatattaatatataaaa---------atatatatataaatatatatataaatatatataa -ataaatatatataaatatatatataaat--atatataaatatatataaatatatatataa -atatatataaatatatataaatatatatataaatatatatataaatatatataaatatat -ataaataaatatataaatatatatataaatatatataaatatatatataaatatatataa -atatatatataaatatatataaatatatatataaatatatataaat--------atatat -ataaatatatatataaatatatataaatatatataaatatatatatataaatatatataa -atatatatataaatataaatatatataaatatataaaaatatatatataaatataaatat -atataaatatatatgtataaatatatatataaatataaatatatataaatatatatatat -aaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaat -atatatataaatatatataaatatatatataaatatatataaaaatatatatatattttt -ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct -tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaa ->p:HG002_2_chr20:14861837-14862841 -gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt -attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac -attggaggttttatatataaatatatatatatatttatatatatatttatatatatatat -atttatatatatttatatatatatttatatatatatttatatatatatttatatatatat -ttatatatatatttatatatatatttatatatatatttatatatatatttatatatattt -atatatatttatatatatttttatatatttttatatatataaatatataaaaatatatat -aaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaat -atatataaatatatatttatatataaatatatataaatatatatttatacataaatatat -ataaatatatatttatacataaatatataaatatatataatatatataaatatatattat -acataaatatataaatatatattatacataaatatataaatatatataaatatatataaa -tatatatttatacataaatatataaatatatatataaatatatataaatatatataaata -tatatataaatatatatataaatatatataaatatatatataaatatatatataaatata -tataaatatatataaatatatatataaatatatataaatatatataaatatatatttata -tattaatatataaatatatataaatatatatttatatattaatatataaatatatatata -ttaatatatataaatatatataaatatatatttatatattaatatatatatattaatata -tatatatttatatattaatatatatatttatatattaatatatataaatatattactatg -tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata -tatattaatatataaaatatatatataaatataaataaatatatatataaatatatataa -ataaatatatatataaatatatataaataaatatataaatatatataaatatatatataa -atatatataaatatatataaatatatataaaaatatatataaatatatatataaatatat -ataaatatatatataaatatatatataaatatatatataaatatatataaatatatatat -aaatatatataaatatatatataattatatataaatatatataaatatatataaatatat -atataaatatatataaatatatataaatatatataaatatatatataaatatatataaat -atatatatataaatatatataaatatatatataaatatatataaatatatatatataaat -atatataaatatatatataaatatatataaatatatatataaatataaatatatatgtat -aaatatatatataaatataaatatatatgtataaatatatatataaatatatatatataa -atatatatatacatatataaatatatatataaatatatataaaaatatatatatatatat -ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct -tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaa ->ref_chr20:14861837-14862841 -gctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatggt -attatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaataggac -attggaggttttatatataaatatatatatatatatttatatatatatttatatatatat -atttatatatatt----------------------------------------------- ----------------tatatatatttatatatatatttatat------------------ ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------atatataaatatatataaatatataaatatat -ataaatatatatttatacataaatatataaatatata----------------------- -----atatatataaatatatattatacataaatatataaatatatataaatatatataaa -tatatatttatacataaatatataaatatat------atatatataaatatatataa--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------atatatatttatatattaatatatataaatatattactatg -tatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaata -tatattaatatataaaa---------atatatat-------------------------- -ataaatatatataaatatatatataaat--atatataaat-------------------- ------------------------------------------------------------- ---------------------------------------atatatatataaatatatataa -atatatatataaatatatataaatatatatataaatatatataaat--------atatat -atataaatatatataa----------------------atatatatataaatatatataa -atatatatataaatataaatatatataaatatataaaaatatatatataaatataaatat -atataaatatatatgtataaatatatatataaatataaatatatataaatatatatatat -aaatatatatataaat------------------------------atatatatataaat -atatatataaatatatataaatatatatataaatatatataaatatatatatatatattt -ttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcct -tttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagca -gaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b0cda8e6691f442d47063f1c6ee4134f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b0cda8e6691f442d47063f1c6ee4134f.msa deleted file mode 100644 index e14ec343..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b0cda8e6691f442d47063f1c6ee4134f.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:63559187-63560064 -gtgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctctt -caggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgc -tgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtgg -tctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcaggg -tcaggtgggag----------------------------------------tcagtcagg -gtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcag -ggtcaggtgggaggagtcagggtcaggt---cggagtcagggtcaggtgggaggagtcag -ggtcaggtgggagtcagtcagggtcaggtgggagg------------------------- ------------------------------------------------------agtcagg -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcag -agtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggt -caggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctgga -agagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagcca -cattcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtgg -gccgctggtccaggtcgctcttggcacaggtgcggacg ->syndip_2_chr20:63559187-63560064 -gtgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctctt -caggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgc -tgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtgg -tctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga---------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------ggagtcagggtcaggtgggaggagtcag -ggtcaggtgggagtc--------------------------------------------- ------------------------------------------------------agtcagg -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcag -ggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggt -caggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctgga -agagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagcca -cattcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtgg -gccgctggtccaggtcgctcttggcacaggtgcggacg ->p:HG002_1_chr20:63559187-63560064 -gtgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctctt -caggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgc -tgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtgg -tctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtggga---------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------ggagtcagggtcaggtgggaggagtcag -ggtcaggtgggagtc--------------------------------------------- ------------------------------------------------------agtcagg -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcag -ggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggt -caggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctgga -agagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagcca -cgttcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtgg -gccgctggtccaggtcgctcttggcacaggtgcggacg ->p:HG002_2_chr20:63559187-63560064 -gtgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctctt -caggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgc -tgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtgg -tctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcaggg -tcaggtgggag----------------------------------------tcagtcagg -gtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcag -ggtcaggtgggaggagtcagggtcaggt---cggagtcagggtcaggtgggaggagtcag -ggtcaggtgggagtcagtcagggtcaggtgggagg------------------------- ------------------------------------------------------agtcagg -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcag -agtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggt -caggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctgga -agagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagcca -cgttcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtgg -gccgctggtccaggtcgctcttggcacaggtgcggacg ->ref_chr20:63559187-63560064 -gtgggggggccctggactttccctcccagtcctggcaccttgcaggtggagagggctctt -caggaaggcatagttggcctcctgcagacgcgcacctggccggcaggcacgagggtctgc -tgagcctcgcagaagtccaggaggctacgccagagggggcagcagcgcagaaggaggtgg -tctcctgtgagggtgggagtcagatgggagtcagtcagggtcaggtgggaggagtcaggg -tcaggtgggaggagtcagggtcaggtgggagtcagtcagggtcaggtgggaggagtcagg -gtcaggtgggaggagtcagggtcagatgggagtcagtcagagtcaggtgggaggagtcag -ggtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtgggaggagtcag -ggtcagatgggagtcagtcagagtcaggtgggaggagtcagggtcaggtgggaggagtca -gggtcaggtcggagtcagggtcaggtgggaggagtcagggtcaggtgggagtcagtcagg -gtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcagatgggagtcagtcag -agtcaggtgggaggagtcagggtcaggtgggaggagtcagggtcaggtcggagtcagggt -caggcaggagtcggcagctccctagcccagccctggcctcacctgtgttcccaccctgga -agagcccagccccgccctcaccgatcaggcagagcccctcctgggcccgcgtgacagcca -cattcacttggttggggtccacaacgaagcccagaaacttcttgagccagctcttggtgg -gccgctggtccaggtcgctcttggcacaggtgcggacg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b11a125770ed30e2b1874895b440ee6f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b11a125770ed30e2b1874895b440ee6f.msa deleted file mode 100644 index 3da102bc..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b11a125770ed30e2b1874895b440ee6f.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:32722323-32723313 -gacagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccc -tcagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttct -ggccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagat -cacctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctacta -aaaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaagg -ctgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgc -cactgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggc -cgagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatca -cgaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaa -atacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggct -gaggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactg -cactccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataa -ata-------aataataataataataataaagacttgtgatcctctccctctccctctcc -ctctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgt -ctccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgc -tgccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgc -ctgcgattgcaggcacgcgccgccacgcctgactggtt ->syndip_2_chr20:32722323-32723313 -gacagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccc -tcagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttct -ggccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagat -cacctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctacta -aaaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaagg -ctgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgc -cactgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggc -cgagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatca -cgaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaa -atacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggct -gaggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacaccactg -cactccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataa -ataaataaataataataataataataataaagacttgtgatcctctccctctccctctcc -ctctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgt -ctccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgc -tgccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgc -ctgcgattgcaggcacgcgccgccacgcctgactggtt ->p:HG002_1_chr20:32722323-32723313 -gacagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccc -tcagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttct -ggccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagat -cacctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctacta -aaaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaagg -ctgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgc -cactgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggc -cgagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatca -cgaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaa -atacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggct -gaggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacaccactg -cactccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataa -ata-------aataataataataataataaagacttgtgatcctctccctctccctctcc -ctctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgt -ctccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgc -tgccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgc -ctgcgattgcaggcacgcgccgccacgcctgactggtt ->p:HG002_2_chr20:32722323-32723313 -gacagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccc -tcagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttct -ggccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagat -cacctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctacta -aaaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaagg -ctgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgc -cactgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggc -cgagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatca -cgaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaa -atacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggct -gaggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactg -cactccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataa -ata-------aataataataataataataaagacttgtgatcctctccctctccctctcc -ctctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgt -ctccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgc -tgccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgc -ctgcgattgcaggcacgcgccgccacgcctgactggtt ->ref_chr20:32722323-32723313 -gacagaggtctcctgaaaattagtgcccataacaggtgtttggtagacaggtctcagccc -tcagacaaacccatttccaaagatgaaggccagagaatgagaataatgatttatcgttct -ggccgggtgtgatggctcatgcctgtaatcccagcgctgtgggaggcgtggccggcagat -cacctgaggtcaggagttcaagaccagcctggccaacatggtgaaacttggtctctacta -aaaatacaaaaattagccaggcatggtggtgggcgcctgcaatcccagctacccagaagg -ctgagtcagaagaatcacttgaacccgggaggtggaggttgcagtgagccgagatcgtgc -cactgcactccagcctgggtgacagagtgagactcaggaaaaaaaaaaaaaagacttggc -cgagcccagtggctcacacctgtaatcccagcactttgggaggctgaggcgggtggatca -cgaggtcaagagatcgagaccatcctggctaacacggtgaaaccccatctctactaaaaa -atacaaaaaattagccgggcgtggtggtgggcacctgtagtcccagctactcgggaggct -gaggcagaatggcgtgaacctggtaggcagagcttgcagtgagctgagatcacgccactg -cactccagcctgggtgacagagcaagactccatctcaaaaataaataaataaataaataa -ata-------aataataataataataataaagacttgtgatcctctccctctccctctcc -ctctccgtctccctctccctctccctctccctccctctccgtctccgtctccgtctccgt -ctccctctccctctccccacggtctccctctcatgcggagccgaagctggactgtactgc -tgccatctcggctcactgcaacctccctgcctgattctcctgcctcagcctgccgagtgc -ctgcgattgcaggcacgcgccgccacgcctgactggtt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b179a5501273075e792cbf44d023019b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b179a5501273075e792cbf44d023019b.msa deleted file mode 100644 index 0b5b5c0f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b179a5501273075e792cbf44d023019b.msa +++ /dev/null @@ -1,350 +0,0 @@ ->syndip_1_chr20:38462831-38464883 -caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc -tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca -agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat -ataaatatatatttatatatatttatatataatatattatatataaatatatttatatat -aatatattatatataaatatattatatataaaatattatatataaatatatatatttata -tatataaatatatataaatatatatatatataaaaataccagcacatcagtatcaggaat -aaatgggctgggcagtatatatatatatatatatgtatatatatatactgtttttcatat -atatatactgtcttatatatatatatactgttttacatatatatactgtttcatatatat -aatgttttatatatatactgttatatatattatatgtactgttatatattttttatatat -atactgttatatatattttttatatatactgttatatattatatatatactgttatatat -atattttacatatatactgttatatatatattttatatatatatactgttatatatatat -attttatatatgtatactgttatatatttatattttttatatgtatactgttatatatat -attatatgtatactgttatatatatattttatatgtatactgttatatatatatatttca -tatatatatactgttatatatattttatatatatatactgtcatatatatattttatata -tatactgtcatatatatattttatatatatatactgtcatatatatattttatatatata -tatactgtcatatatatattttatatatatatactgtcatatatattttatatatatact -gtcatatatatattttatatatatactgtcatatatatattttatatatatactgtcata -tatatattt--tatatatatactgtcatatatatattttatatatatatactgtcatata -tatattttatatatatatactgtcatatatatattttatatatatactgtcatatgtata -ttttatatatatactgtcatatgtatattt------------------------------ --tatatatatactgttatatgtatattttatatatatatactgttatatatatattttta -tatatatactgttatatatatttttttatatatatactgttatatatatttttatatata -tactgttatatatatattttatatatatactgttatatatatattttatatatactgtta -tatatatatattttatatatatactgttatatataatttttttcatatatatactgttat -atatatattttatatatatatactgttatatatatattttatatatatactgttatatat -atatattttatatatatactgttattttttatatatatactgttatatatatattttata -tatatactgttatatatatattatctatatactgttatgtgtatattttatctatatact -gttatgtgtatattttatctatatactgttatgtgtatattttacctatatacttttatg -tgtatattttatatatatactgttatgtgtatattttatatatatactgttatgtgtata -ttttttatatatactgttatgtgtatattttatatatatatactgttatgtgtatatttt -atatatatatactgttatgtgtatattttatatatatactgttatgtgtatattttatat -atatactgttatatatagttcatatatatactgttatatgtatagttcatatatatactg -ttatatatatagttcatatgtatactgttatatatatagttcatatatatactgttatat -atatagttcatatatatactgttatatatatatagttcatatatatactgttatatatag -ttcatatatatactgttatatatatagttcatatatatactgttatatatatagttcata -tatatactgttatatatagttcatatatatatactgttctatatatagttcatatatata -tactgttatatatatagttcatatatatatactgttatatatagttcatatatatatagt -tcatatatatactgttatatatatagttcatatatatactgttatatacatagttcatat -atatactgttatatatatagttcatatatatatactgttatatatatagttcatatatat -actgttgtatatagttcatatatatactgttatatatatagttcatatattactgttata -tatatagttcatatatatactgttatatatatatagttcatatatatactgttatatata -gtttatatatatatactgttatatatatagtttatatatatatactgttatatatatagt -ttatatatatatactgttatatatatatagtttatatatatatactgttatatatatagt -ttatatatatatactgttatatatatatagtttatatatactgttatatatatagtttat -atatatactgttatatatatagtttatatatatactgttatatatatagtttatatatat -actgttatatatatagtttatatatatactgttatatatatagtttatatatatactgtt -atatatatagtttatatatatactgttatatatatagtttatatatatatactgt--tat -atatagtttatatatactgttatatatatagtttatatactgttatatatagtttatata -tatatactgttatatatagtttatatatatatactgttatatatatatagtttatatata -tatactgttatatatatatagtttatatatatactgttatatatatatagtttatatata -tactgttgtatatatagtttatatatatactgttatatatatatttgtgtatatatactg -ttatataaatatatttgtgtatatatactgttatatatatattttatgtatatatactgt -tatatatatattttatgtatatatactgttatatatatattttatgtatatatactgtta -tatatatattttatgtatatatactgttatatatatattttatgtatatatactgttata -tatattttatgtatatatactgttatatatattttatgtatatatactgttatatatata -ttttatgtatatatactgttatatctgtatattttatgtttatatactgttatatctgta -tattttatgtatatatactgttatatctgtatattttatgtatatactgttatatatata -ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta -tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata -ctgttatatatattgttatatatatacacatatatatatac--atatatatacatatata -tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata -tatatatatacacacacatatatatatatatatatactggctgtgtgtggtggtgcacac -ctgtaatcccagcactttgggaggccaaggcaggctgatggcttgagctcaggagttcaa -gaccagctaagcaacatactgagatcccatctctaaaaaaaatacaaaaaggccaggcac -agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc -agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa -cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg -agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaa- ->syndip_2_chr20:38462831-38464883 -caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc -tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca -agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat -ataaatatatatttatatatatttatatataatatattatatat-aatatatttatatat -aatatattatatataaatatattatatataaaatattatatataaatatatatatttata -tatataaatatatataaatatatatatatataaaaataccagcacatcagtatcaggaat -aaatgggctgggcag--tatatatatatatatatgtatatatatatactgtttttcatat -atatatactgtcttatatatatatatactgttttacatatatatactgtttcatatatat -aatgttttatatatatactgttatatatattatatgtactgttatatattttttatatat -atactgttatatatattttttatatatactgttatatattatatatatactgttatatat -atattttacatatatactgttatatatatattttatatatatatactgttatatatatat -attttatatatgtatactgttatatatttatattttttatatgtatactgttatatatat -attatatgtatactgttatatatatattttatatgtatactgttatatatatatatttca -tatatatatactgttatatatattttatatatatatactgtcatatatatattttatata -tatactgtcatatatatattttatatatatatactgtcatatatatattt--tatatata -tatactgtcatatatatattttatatatatatactgtcatatatattttatatatatact -gtcatatatatattttatatatatactgtcatatatatattttatatatatactgtcata -tatatattttatatatatatactgtcatatatatattttatatatatatactgtcatata -tatattt--tatatatatactgtcatatgtatattttatatatatactgtcatatgtata -ttttatatatatactgttatatgtatattttatatatatatactgttatatatatatttt -atatatatatactgttatatatatattttatatatatatactgttatatatatattttta -tatatatactgttatatatatttttttatatatatactgttatatatatttttatatata -tactgttatatatatattttatatatatactgttatatatatattttatatatactgtta -tatatatatattttatatatatactgttatatataatttttttcatatatatactgttat -atatatattttatatatatatactgttatatatatattttatatatatactgttatatat -atatattttatatatatactgttattttttatatatatactgttatatatatattttata -tatatactgttatatatatattatctatatactgttatgtgtatattttatctatatact -gttatgtgtatattttatctatatactgttatgtgtatattttacctatatacttttatg -tgtatattttatatatatactgttatgtgtatattttatatatatactgttatgtgtata -ttttttatatatactgttatgtgtatattttatatatatatactgttatgtgtatatttt -atatatatatactgttatgtgtatattttatatatatactgttatgtgtatattttatat -atatactgttatatatagttcatatatatactgttatatgtatagttcatatatatactg -ttatatatatagttcatatgtatactgttatatatatagttcatatatatactgttatat -atatagttcatatatatactgttatatatatatagttcatatatatactgttatatatag -ttcatatatatactgttatatatatagttcatatatatactgttatatatatagttcata -tatatactgttatatatagttcatatatatatactgttctatatatagttcatatatata -tactgttatatatatagttcatatatatatactgttatatatagttcatatatatatagt -tcatatatatactgttatatatatagttcatatatatactgttatatacatagttcatat -atatactgttatatatatagttcatatatatatactgttatatatatagttcatatatat -actgttgtatatagttcatatatatactgttatatatatagttcatatattactgttata -tatatagttcatatatatactgttatatatatatagttcatatatatactgttatatata -gtttatatatatatactgttatatatatagtttatatatatatactgttatatatatagt -ttatatatatatactgttatatatatatagtttatatatatatactgttatatatatagt -ttatatatatatactgt--tatatatatagtttatatatactgtta-------------- ------------tatatatatagtttatatatatactgttatatatatagtttatatatat -actgttatatatatagtttatatatatactgttatatatatagtttatatatatactgtt -atatatatagtttatatatatactgttatatatatagtttatatatatatactgttatat -atatagtttataaatactgttatatatatagtttatatactgttatatatagtttatata -tatatactgttatatatagtttatatatatatactgttatatatatatagtttatatata -tatactgttatatatatatagtttatatatatactgttatatatatatagtttatatata -tactgttgtatatatagtttatatatatactgttatatatatatttgtgtatatatactg -ttatataaatatatttgtgtatatatactgttatatatatattttatgtatatatactgt -tatatatatattttatgtatatatactgttatatatatattttatgtatatatactgtta -tatatatattttatgtatatatactgtta---------------------------tata -tatattttatgtatatatactgttatatatattttatgtatatatactgttatatatata -ttttatgtatatatactgttatatctgtatattttatgtttatatactgttatatctgta -tattttatgtatatatactgttatatctgtatattttatgtatatactgttatatatata -ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta -tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata -ctgttatatatattgttatatatatacacat------------atatatatacatatata -tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata -tatatatatacacacacatatatatatatatatatactggctgtgtgtggtggtgcacac -ctgtaatcccagcactttgggaggccaaggcaggctgatggcttgagctcaggagttcaa -gaccagctaagcaacatactgagatcccatctctaaaaaaaatacaaaaaggccaggcac -agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc -agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa -cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg -agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaaa ->p:HG002_1_chr20:38462831-38464883 -caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc -tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca -agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat -ataaatatatatttatatatatttatatataatatattatatat-aatatatttatatat -aatatattatatataaatatattatatataaaatattatatataaatatatatatttata -tatataaatatatataaatatatatatatataaaaataccagcacatcagtatcaggaat -aaatgggctgggcag--tatatatatatatatatgtatatatatatactgtttttcatat -atatatactgtcttatatatatatatactgttttacatatatatactgtttcatatatat -aatgttttatatatatactgttatatatattatatgtactgttatatattttttatatat -atactgttatatatattttttatatatactgttatatattatatatatactgttatatat -atattttacatatatactgttatatatatattttatatatatatactgttatatatatat -attttatatatgtatactgttatatatttatattttttatatgtatactgttatatatat -attatatgtatactgttatatatatattttatatgtatactgttatatatatatatttca -tatatatatactgttatatatattttatatatatatactgtcatatatatattttatata -tatactgtcatatatatattttatatatatatactgtcatatatatattt--tatatata -tatactgtcatatatatattttatatatatatactgtcatatatattttatatatatact -gtcatatatatattttatatatatactgtcatatatatattttatatatatactgtcata -tatatattttatatatatatactgtcatatatatattttatatatatatactgtcatata -tatattt--tatatatatactgtcatatgtatattttatatatatactgtcatatgtata -ttttatatatatactgttatatgtatattttatatatatatactgttatatatatatttt -atatatatatactgttatatatatattttatatatatatactgttatatatatattttta -tatatatactgttatatatatttttttatatatatactgttatatatatttttatatata -tactgttatatatatattttatatatatactgttatatatatattttatatatactgtta -tatatatatattttatatatatactgttatatataatttttttcatatatatactgttat -atatatattttatatatatatactgttatatatatattttatatatatactgttatatat -atatattttatatatatactgttattttttatatatatactgttatatatatattttata -tatatactgttatatatatattatctatatactgttatgtgtatattttatctatatact -gttatgtgtatattttatctatatactgttatgtgtatattttacctatatacttttatg -tgtatattttatatatatactgttatgtgtatattttatatatatactgttatgtgtata -ttttttatatatactgttatgtgtatattttatatatatatactgttatgtgtatatttt -atatatatatactgttatgtgtatattttatatatatactgttatgtgtatattttatat -atatactgttatatatagttcatatatatactgttatatgtatagttcatatatatactg -ttatatatatagttcatatgtatactgttatatatatagttcatatatatactgttatat -atatagttcatatatatactgttatatatatatagttcatatatatactgttatatatag -ttcatatatatactgttatatatatagttcatatatatactgttatatatatagttcata -tatatactgttatatatagttcatatatatatactgttctatatatagttcatatatata -tactgttatatatatagttcatatatatatactgttatatatagttcatatatatatagt -tcatatatatactgttatatatatagttcatatatatactgttatatacatagttcatat -atatactgttatatatatagttcatatatatatactgttatatatatagttcatatatat -actgttgtatatagttcatatatatactgttatatatatagttcatatattactgttata -tatatagttcatatatatactgttatatatatatagttcatatatatactgttatatata -gtttatatatatatactgttatatatatagtttatatatatatactgttatatatatagt -ttatatatatatactgttatatatatatagtttatatatatatactgttatatatatagt -ttatatatatatactgt--tatatatatagtttatatatactgtta-------------- ------------tatatatatagtttatatatatactgttatatatatagtttatatatat -actgttatatatatagtttatatatatactgttatatatatagtttatatatatactgtt -atatatatagtttatatatatactgttatatatatagtttatatatatatactgttatat -atatagtttataaatactgttatatatatagtttatatactgttatatatagtttatata -tatatactgttatatatagtttatatatatatactgttatatatatatagtttatatata -tatactgttatatatatatagtttatatatatactgttatatatatatagtttatatata -tactgttgtatatatagtttatatatatactgttatatatatatttgtgtatatatactg -ttatataaatatatttgtgtatatatactgttatatatatattttatgtatatatactgt -tatatatatattttatgtatatatactgttatatatatattttatgtatatatactgtta -tatatatattttatgtatatatactgtta---------------------------tata -tatattttatgtatatatactgttatatatattttatgtatatatactgttatatatata -ttttatgtatatatactgttatatctgtatattttatgtttatatactgttatatctgta -tattttatgtatatatactgttatatctgtatattttatgtatatactgttatatatata -ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta -tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata -ctgttatatatattgttatatatatacacat------------atatatatacatatata -tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata -tatatatatacacacacatatatatatatatatatactggctgtgtgtggtggtgcacac -ctgtaatcccagcactttgggaggccaaggcaggctgatggcttgagctcaggagttcaa -gaccagctaagcaacatactgagatcccatctctaaaaaaaatacaaaaaggccaggcac -agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc -agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa -cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg -agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaaa ->p:HG002_2_chr20:38462831-38464883 -caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc -tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca -agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat -ataaatatatatttatatatatttatatataatatattatatataaatatatttatatat -aatatattatatataaatatattatatataaaatattatatataaatatatatatttata -tatataaatatatataaatatatatatatataaaaataccagcacatcagtatcaggaat -aaatgggctgggcagtatatatatatatatatatgtatatatatatactgtttttcatat -atatatactgtcttatatatatatatactgttttacatatatatactgtttcatatatat -aatgttttatatatatactgttatatatattatatgtactgttatatattttttatatat -atactgttatatatattttttatatatactgttatatattatatatatactgttatatat -atattttacatatatactgttatatatatattttatatatatatactgttatatatatat -attttatatatgtatactgttatatatttatattttttatatgtatactgttatatatat -attatatgtatactgttatatatatattttatatgtatactgttatatatatatatttca -tatatatatactgttatatatattttatatatatatactgtcatatatatattttatata -tatactgtcatatatatattttatatatatatactgtcatatatatattttatatatata -tatactgtcatatatatattttatatatatatactgtcatatatattttatatatatact -gtcatatatatattttatatatatactgtcatatatatattttatatatatactgtcata -tatatattt--tatatatatactgtcatatatatattttatatatatatactgtcatata -tatattttatatatatatactgtcatatatatattttatatatatactgtcatatgtata -ttttatatatatactgtcatatgtatattt------------------------------ --tatatatatactgttatatgtatattttatatatatatactgttatatatatattttta -tatatatactgttatatatatttttttatatatatactgttatatatatttttatatata -tactgttatatatatattttatatatatactgttatatatatattttatatatactgtta -tatatatatattttatatatatactgttatatataatttttttcatatatatactgttat -atatatattttatatatatatactgttatatatatattttatatatatactgttatatat -atatattttatatatatactgttattttttatatatatactgttatatatatattttata -tatatactgttatatatatattatctatatactgttatgtgtatattttatctatatact -gttatgtgtatattttatctatatactgttatgtgtatattttacctatatacttttatg -tgtatattttatatatatactgttatgtgtatattttatatatatactgttatgtgtata -ttttttatatatactgttatgtgtatattttatatatatatactgttatgtgtatatttt -atatatatatactgttatgtgtatattttatatatatactgttatgtgtatattttatat -atatactgttatatatagttcatatatatactgttatatgtatagttcatatatatactg -ttatatatatagttcatatgtatactgttatatatatagttcatatatatactgttatat -atatagttcatatatatactgttatatatatatagttcatatatatactgttatatatag -ttcatatatatactgttatatatatagttcatatatatactgttatatatatagttcata -tatatactgttatatatagttcatatatatatactgttctatatatagttcatatatata -tactgttatatatatagttcatatatatatactgttatatatagttcatatatatatagt -tcatatatatactgttatatatatagttcatatatatactgttatatacatagttcatat -atatactgttatatatatagttcatatatatatactgttatatatatagttcatatatat -actgttgtatatagttcatatatatactgttatatatatagttcatatattactgttata -tatatagttcatatatatactgttatatatatatagttcatatatatactgttatatata -gtttatatatatatactgttatatatatagtttatatatatatactgttatatatatagt -ttatatatatatactgttatatatatatagtttatatatatatactgttatatatatagt -ttatatatatatactgttatatatatatagtttatatatactgttatatatatagtttat -atatatactgttatatatatagtttatatatatactgttatatatatagtttatatatat -actgttatatatatagtttatatatatactgttatatatatagtttatatatatactgtt -atatatatagtttatatatatactgttatatatatagtttatatatatatactgt--tat -atatagtttatatatactgttatatatatagtttatatactgttatatatagtttatata -tatatactgttatatatagtttatatatatatactgttatatatatatagtttatatata -tatactgttatatatatatagtttatatatatactgttatatatatatagtttatatata -tactgttgtatatatagtttatatatatactgttatatatatatttgtgtatatatactg -ttatataaatatatttgtgtatatatactgttatatatatattttatgtatatatactgt -tatatatatattttatgtatatatactgttatatatatattttatgtatatatactgtta -tatatatattttatgtatatatactgttatatatatattttatgtatatatactgttata -tatattttatgtatatatactgttatatatattttatgtatatatactgttatatatata -ttttatgtatatatactgttatatctgtatattttatgtttatatactgttatatctgta -tattttatgtatatatactgttatatctgtatattttatgtatatactgttatatatata -ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta -tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata -ctgttatatatattgttatatatatacacatatatatatac--atatatatacatatata -tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata -tatatatatacacacacatatatatatatatatatactggctgtgtgtggtggtgcacac -ctgtaatcccagcactttgggaggccaaggcaggctgatggcttgagctcaggagttcaa -gaccagctaagcaacatactgagatcccatctctaaaaaaaatacaaaaaggccaggcac -agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc -agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa -cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg -agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaa- ->ref_chr20:38462831-38464883 -caccatgttacctaggctgatcttgaattcctgggctcaagtgttagactcacttcggcc -tcccaaagtgttgggattacaggcgtgagccactgcacccagcctgttttgtttggggca -agggttttaacatttatatatatataaatatatatatattttatatatacaaatatatat -ataaatatatatttatatatatttatatataatatattatatataaatatatttatatat -aatatattatatataaatatattatatataaaatattatatataaatatatatatttata -tatataaatatatataaatatatatatatataaaaataccagcacatcagtatcaggaat -aaatgggctgggcagtatatatatatatatatatgtatatatatatactgtttttcatat -atatatactgtcttatatatatatatactgttttacatatatatactgtttcatatatat -aatgttttatatatatactgttatatatattatatgtactgttatatattttttatatat -atactgttatatatattttttatatatactgttatatattatatatatactgttatatat -atattttacatatatactgttatatatatattttatatatatatactgttatatatatat -attttatatatgtatactgttatatatttatattttttatatgtatactgttatatatat -attatatgtatactgttatatatatattttatatgtatactgttatatatatatatttca -tatatatatactgttatatatattttatatatatatactgtcatatatatattttatata -tatactgtcatatatatattttatatatatatactgtcatatatatattttatatatata -tatactgtcatatatatattttatatatatatactgtcatatatattttatatatatact -gtcatatatatattttatatatatactgtcatatatatattttatatatatactgtcata -tatatattt--tatatatatactgtcatatatatattttatatatatatactgtcatata -tatattttatatatatatactgtcatatatatattttatatatatactgtcatatgtata -ttttatatatatactgtcatatgtatattt------------------------------ --tatatatatactgttatatgtatattttatatatatatactgttatatatatattttta -tatatatactgttatatatatttttttatatatatactgttatatatatttttatatata -tactgttatatatatattttatatatatactgttatatatatatttta------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------tatatactgttatatagata -ctgttatatatatactgatatatatactgttatatatatactgatatatatatactgtta -tatatatactgttatatatatatactgttacatatacatatatatactgttatatatata -ctgttatatatattgttatatatatacacatatatatatacatatatatatacatatata -tatacatatatatatacatatatatatacacgtatatatatacatatatatatacacata -tatatatatacacacacatatatatatatatatatactggctgtgtgtggtggtgcacac -ctgtaatcccagcactttgggaggccaaggcaggctgatggcttgagctcaggagttcaa -gaccagctaagcaacatactgagatcccatctctaaaaaaaatacaaaaaggccaggcac -agtggctcacacctgtaatcccagcactttgggaggctgaggtgggcagatcacgaggtc -agcagttcgagaccagcctggccagcatggtgaaaccccatctctactaaaaatacaaaa -cattagccggacatggtggcacacacctgtaattccagctactcaggaagctgaggcagg -agaatagcttgaacccaggaggcgaaagtttcagtcagccaaaatcacaccactgcactc -cagcctgggcaacagagcaagactctgtctccaaaaaa- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b179aed9eca36907c850db7596e36ef6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b179aed9eca36907c850db7596e36ef6.msa deleted file mode 100644 index d4c93ce2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b179aed9eca36907c850db7596e36ef6.msa +++ /dev/null @@ -1,180 +0,0 @@ ->syndip_1_chr20:38123489-38124806 -tttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgt -ggatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcct -gtcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatata -ataatatataataataatatataatatgtataataataatatataatatttataataata -atatatataatatgtatatataatatacatatacctattatatataatatacctattata -tataatatacatatacctattatatataatatacctattatatataagatacctattata -tataatatacatatacctattatatatataatatacctattatatatatataatatacct -attatatataatatacctattatatatataatatacctattatatatataatatacctat -tatatatataatatacctattatatataatatacctattatatataaaatatacctatta -tatataatatacctattatatacattatatataatatacctattatatgcattatatata -atatacctattatatgcattatatataatatacctattatatgcattatatataatatac -ctattatatgcattatatataatatacctattatatgcattatataatatattatatata -atatgcatattatatgtattatatattatatattatatatataatatacatattatatgt -attatatattatatattatatatataatatacatattatatgtattatatattatatata -atatacatattatatattatatattatatacatattatatattatatattatatacatat -tatatattatatacatattatatattatatattatatacatattatacattatatatatc -taaaatatataatacacattatatattatataatacacattatatataatatataataca -cattatatattatatataatacacattatatattatatataatacacattatatat---- --------------------tatataatacacattatatattatatataatacacattata -tattatatataatacacattatatattatatataatacacattatatattatataataca -cattatatattatatataatacacattatatatataatacacattatatattatatataa -tacataatacacattatatattatatataatacacattatatataatatataacacacat -tatatataatatataacacacattatatattatatataatacacattatatattatatat -aatacacatatattatatataatacacattatatattatatataatacacatatattata -tataatacacattatatattatatataatacacattatatataatatataatacacatta -tatataatacttattatatattatacataatatacatattatatataatacataatatac -gtatattatataatatacatattatatataatacataatatacgtatattatataatata -catattatatatattatactatatataatactcatatatatacatattatatatacatat -tatatataatactcatattatatgtacatattatacatacatattatatataatacacat -atatacatattatatataatacacacacacattatatatgtcttatatataatatacata -ttatatatgtattatattattatagatataatatacatattatatctatatataaaatat -atatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgc -aatcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagcccc -ccgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttatttttt -gtagagatggggtttcgccatgttgccgaggctggtgtcaa ->syndip_2_chr20:38123489-38124806 -tttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgt -ggatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcct -gtcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatata -ataatatataataataatatataatatgtataataataatatataatatttataataata -atatatataatatgtatatataatatacatatacctattatatataatatacctattata -tataatatacatatacctattatatataatatacctattatatataagatacctattata -tataatatacatatacctattatatatataatatacctattatatatatataatatacct -attatatataatatacctattatatatataatatacctattatatatataatatacctat -tatatatataatatacctattatatataatatacctattatatataaaatatacctatta -tatataatatacctattatata---------------------------cattatatata -atatacctattatatgcattatatataatatacctattatatgcattatatataatatac -ctattatatgcattatatataatatacctattatatgcattatataatatattatatata -atatgcatattatatgtattatatattatatattatatatataatatacatattatatgt -attatatattatatattatatatataatatacatattatatgtattatatattatatata -atatacatattatatattatatattatatacatattatatattatatattatatacatat -tatatattatatacatattatatattatatattatatacatattatacattatatatatc -taaaatatataatacacattatatattatataatacacattatatataatatataataca -cattatatattatatataatacacattatatattatatataatacacattatatattata -taatacacattatatattatatataatacacattatatattatatataatacacattata -tattatatataatacacattatatattatatataatacacattatatattatataataca -cattatatattatatataatacacattatatatataatacacattatatattatatataa -tacataatacacattatatattatatataatacacattatatataatatataacacacat -tatatataatatataacacacattatatattatatataatacacattatatattatatat -aatacacatatattatatataatacacattatatattatatataatacacatatattata -tataatacacattatatattatatataatacacattatatataatatataatacacatta -tatataatacttattatatattatacataatatacatattatatataatacataatatac -gtatattatataatatacatattatatataatacataatatacgtatattatataatata -catattatatatattatactatatataatactcatatatatacatattatatatacatat -tatatataatactcatattatatgtacatattatacatacatattatatataatacacat -atatacatattatatataatacacacacacattatatatgtcttatatataatatacata -ttatatatgtattatattattatagatataatatacatattatatctatatataaaatat -atatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgc -aatcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagcccc -ccgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttatttttt -gtagagatggggtttcgccatgttgccgaggctggtgtcaa ->p:HG002_1_chr20:38123489-38124806 -tttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgt -ggatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcct -gtcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatata -ataatatataataataatatataatatgtataataataatatataatatttataataata -atatatataatatgtatatataatatacatatacctattatatataatatacctattata -tataatatacatatacctattatatataatatacctattatatataagatacctattata -tataatatacatatacctattatatatataatatacctattatatatatataatatacct -attatatataatatacctattatatatataatatacctattatatatataatatacctat -tatatatataatatacctattatatataatatacctattatatataaaatatacctatta -tatataatatacctattatata---------------------------cattatatata -atatacctattatatgcattatatataatatacctattatatgcattatatataatatac -ctattatatgcattatatataatatacctattatatgcattatataatatattatatata -atatgcatattatatgtattatatattatatattatatatataatatacatattatatgt -attatatattatatattatatatataatatacatattatatgtattatatattatatata -atatacatattatatattatatattatatacatattatatattatatattatatacatat -tatatattatatacatattatatattatatattatatacatattatacattatatatatc -taaaatatataatacacattatatattatataatacacattatatataatatataataca -cattatatattatatataatacacattatatattatatataatacacattatatattata -taatacacattatatattatatataatacacattatatattatatataatacacattata -tattatatataatacacattatatattatatataatacacattatatattatataataca -cattatatattatatataatacacattatatatataatacacattatatattatatataa -tacataatacacattatatattatatataatacacattatatataatatataacacacat -tatatataatatataacacacattatatattatatataatacacattatatattatatat -aatacacatatattatatataatacacattatatattatatataatacacatatattata -tataatacacattatatattatatataatacacattatatataatatataatacacatta -tatataatacttattatatattatacataatatacatattatatataatacataatatac -gtatattatataatatacatattatatataatacataatatacgtatattatataatata -catattatatatattatactatatataatactcatatatatacatattatatatacatat -tatatataatactcatattatatgtacatattatacatacatattatatataatacacat -atatacatattatatataatacacacacacattatatatgtcttatatataatatacata -ttatatatgtattatattattatagatataatatacatattatatctatatataaaatat -atatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgc -aatcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagcccc -ccgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttatttttt -gtagagatggggtttcgccatgttgccgaggctggtgtcaa ->p:HG002_2_chr20:38123489-38124806 -tttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgt -ggatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcct -gtcctgtaacctctctgggcctcagaaacctctctctctctc--tatatatatatatata -ataatatataataataatatataatatgtataataataatatataatatttataataata -atatatataatatgtatatataatatacatatacctattatatataatatacctattata -tataatatacatatacctattatatataatatacctattatatataagatacctattata -tataatatacatatacctattatatatataatatacctattatatatatataatatacct -attatatataatatacctattatatatataatatacctattatatatataatatacctat -tatatatataatatacctattatatataatatacctattatatataaaatatacctatta -tatataatatacctattatatacattatatataatatacctattatatgcattatatata -atatacctattatatgcattatatataatatacctattatatgcattatatataatatac -ctattatatgcattatatataatatacctattatatgcattatataatatattatatata -atatgcatattatatgtattatatattatatattatatatataatatacatattatatgt -attatatattatatattatatatataatatacatattatatgtattatatattatatata -atatacatattatatattatatattatatacatattatatattatatattatatacatat -tatatattatatacatattatatattatatattatatacatattatacattatatatatc -taaaatatataatacacattatatattatataatacacattatatataatatataataca -cattatatattatatataatacacattatatattatatataatacacattatatat---- --------------------tatataatacacattatatattatatataatacacattata -tattatatataatacacattatatattatatataatacacattatatattatataataca -cattatatattatatataatacacattatatatataatacacattatatattatatataa -tacataatacacattatatattatatataatacacattatatataatatataacacacat -tatatataatatataacacacattatatattatatataatacacattatatattatatat -aatacacatatattatatataatacacattatatattatatataatacacatatattata -tataatacacattatatattatatataatacacattatatataatatataatacacatta -tatataatacttattatatattatacataatatacatattatatataatacataatatac -gtatattatataatatacatattatatataatacataatatacgtatattatataatata -catattatatatattatactatatataatactcatatatatacatattatatatacatat -tatatataatactcatattatatgtacatattatacatacatattatatataatacacat -atatacatattatatataatacacacacacattatatatgtcttatatataatatacata -ttatatatgtattatattattatagatataatatacatattatatctatatataaaatat -atatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgc -aatcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagcccc -ccgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttatttttt -gtagagatggggtttcgccatgttgccgaggctggtgtcaa ->ref_chr20:38123489-38124806 -tttttaagtccacagcctgtgaccaatggcaacagagcagaaggttagagcaattactgt -ggatggagcttgcccagtaggcctcctagctccattttctagctttgtgatctcaggcct -gtcctgtaacctctctgggcctcagaaacctctctctctctctatatatatatatatata -ataatatataataataatatataatatgtataataataatatataatatttataataata -atatatataatatgtatatataatatacatatacctattatatataatatacctattata -tataatatacataaacctattatatataatatacctattatatataagatacctattata -tataatatacctat------------------------------tatatataagatacct -attatatataatatac--------------atatacctattatatatataatatacctat -tata----------------tatatataatatacctattatatatataatatacctatta -----------------------------------------------------tatatata -atatacctattatatatataata------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------tacctattatatataatacacattatatataatatataacacacat -tatatataatatataacacacattatatattatatataatacacattatatattatatat -aatacacatatattatatataatacacattatatattatatataatacacatatattata -tataatacacattatatattatatataatacacattatatataatatataatacacatta -tatataatacttattatatattatacataatatacatattatatataatacataatatac -gtatattatataatatacatattatatataatacataatatacgtatattatataatata -catattatatatattatactatatataatactcatatatatacatattatatatacatat -tatatataatactcatattatatgtacatattatacatacatattatatataatacacat -atatacatattatatataatacacacacacattatatatgtcttatatataatatacata -ttatatatgtattatattattatagatataatatacatattatatctatatataaaatat -atatgtagagagagagagacagggtctcattttgtctcccaggctggagtgcagtggtgc -aatcttggctcactacaacctccacctcccaggctcaagggatcctccagcttcagcccc -ccgagtacctgggactacaggaacgcgtcaccatgcctggctaatttttttttatttttt -gtagagatggggtttcgccatgttgccgaggctggtgtcaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b206928da83df6d728521bb51cfc7a4d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b206928da83df6d728521bb51cfc7a4d.msa deleted file mode 100644 index 29d71e41..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b206928da83df6d728521bb51cfc7a4d.msa +++ /dev/null @@ -1,170 +0,0 @@ ->syndip_1_chr20:4032119-4033701 -cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag -cggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaaa -gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct -gcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaa -agt----------------------------------------gaggagcgtctctgccc -ggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagga -agtgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgcccc -accgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtg -aggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaacc -gccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgagg -agcgtctccgcccggcagccaccccgtccgggagggaggtggggggggtcagccccccgc -ccggccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactggga -agtgaggagcccctctgcccggccagccgccccgtccgggagggaggcgggggggggggt -cggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgc -cccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccc -tctgcccggccagccgccccgtccgggagggaggtgggggggtcagtcccccgcccggcc -ggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccg -cctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagcc -gccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgg -gagggaggtggg--ggggggtcagccccccgcccggccagccgccccgtccgggagggag -gtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctct -gcccggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgg -gagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtca -gccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccc -ctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggg -gggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccgg -ccgcccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagggt -agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc -tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg -gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat -agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacat ->syndip_2_chr20:4032119-4033701 -cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag -cggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaaa -gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct -gcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaa -agtgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgccc -ggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagga -actgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgcccc -accgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtg -aggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaacc -gccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgagg -agcgtctccgcccggcagccaccccgtccgggagggaggt-------------------- ------------------------------------------------------------- -------------------------------------------------gggggggggggt -cggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgc -cccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccc -tctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggcc -ggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccg -cctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagcc -gccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgg -gagggaggtgggggggggggtcagccccccgcccggccagccgccccgtccgggagggag -gtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctct -gcccggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgg -gagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtca -gccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccc -ctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggg -gggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccgg -ccgcccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggagggt -agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc -tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg -gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat -agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacat ->p:HG002_1_chr20:4032119-4033701 -cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag -cggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaaa -gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct -gcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaa -agtgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgccc -ggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagga -actgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgcccc -accgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtg -aggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaacc -gccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgagg -agcgtctccgcccggcagccaccccgtccgggagggaggt-------------------- ------------------------------------------------------------- -------------------------------------------------gggggggggggt -cggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgc -cccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccc -tctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggcc -ggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccg -cctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagcc -gccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgg -gagggaggtgggggggggggtcagccccccgcccggccagccgccccgtccgggagggag -gtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctct -gcccggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgg -gagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtca -gccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccc -ctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggg -gggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccgg -ccgcccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggagggt -agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc -tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg -gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat -agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacat ->p:HG002_2_chr20:4032119-4033701 -cgggattgcagatgaagtctcgttcactcagtgctcaatggtgcccaggctggagtgcag -tggcgtgatctccgctcgctacaacctccacctcccagccgcctgccttggcctcccaaa -gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct -gcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaa -agt----------------------------------------gaggagcgtctctgccc -ggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagga -agtgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgcccc -accgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtg -aggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaacc -gccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgagg -agcgtctccgcccggcagccaccccgtccgggagggaggtggggggggtcagccccccgc -ccggccagccgccccgtccgggaggtgaggggctcctctgcccggccgcccctactggga -agtgaggagcccctctgcccggccagccgccccgtccgggagggaggcgggggggggggt -cggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgc -cccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccc -tctgcccggccagccgccccgtccgggagggaggtgggggggtcagtcccccgcccggcc -ggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccg -cctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagcc -gccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgg -gagggaggtggg--ggggggtcagccccccgcccggccagccgccccgtccgggagggag -gtggggggatcagccccccgcctggccagccgccccgtccgggaggtgaggggcgcctct -gcccggccacccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgg -gagggaggcgggggggggggtcggccagccgccccgtccgggagggaggtgggggggtca -gccccccttccggccggccgccctgtccgggaggtgaggggcgcctctgcctggccgccc -ctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggg -gggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccgg -ccgcccctactgggaagtgaggagcccctctgcccggccagccgccccgtccgggagggt -agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc -tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg -gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat -agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacat ->ref_chr20:4032119-4033701 -cgggattgcagatgaagtctcgttcactcagtgctcagtggtgtccaggctggagtgcag -cggcgtgatctcggctcgctacaa---ccacctcccagccgcctgccttggcctcccaaa -gagccgagattgcagcctctgcccggccgccaccccgtctgggaagtgaggagcgtctct -gcttggccacccatcgtctgggatatgaggagcccctctgcctggctgcccagtctggaa -agtgaggagcgtctctgcccggccgccatcccatctaggaagcgaggagcgtctctgccc -ggccgccatcccatctaggaagcgaggagcgcctcttcccggctgccatcccatctagga -actgaggagcgtctctgcccggccgcccatcgtctgagatgtggggagcacctctgcccc -accgccctgtctgggatgtgaggagcgcctctgctgggccgcaaccctgtctgggaggtg -aggagcgtctctgccccgccgctccgtctgagaagtgaggaaaccctctgcctggcaacc -gccccgtctgagaagtgaggagcccctccgtccggcaaccaccccgtctgggaagtgagg -agcgtctccgcccggcagccaccccgtccgggagggaggt-------------------- ------------------------------------------------------------- -------------------------------------------------gggggggggggt -cggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggccggccgc -cccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgaggacccc -tctgcccggccagccgccccgtccgggagggaggtgggggggtcagccccccgcccggcc -ggctgccccgtccgggaggtgaggggcgcctctgcccggccgcccctactgggaagtgag -gagcccctctgcccggccagctgccccgcccgggagggaggtgggggggtcagccccccg -cctggccagccgccccatccgggagggaggtgggggggtcagccccccgcccggccagcc -gccccgtccgggaggggggagggggggtcagccccctgcccggccagccgccccgtccgg -gagggaggtggg------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------gggggggtca -gccccctttccggccg--ccgcctgtccgggaggtgaggggcgcctctgcctggccgccc -ctactgggaagtgaggacccctctgcccggccagccgccccgtccgggagggaggtgggg -gggacagccccccgcccggccagccgccctatccaggaggtgaggggcgcctctgcccgg -ccgcccctactgggaagtgaggagcccctctgcctggccagccgccccgtccgggagggt -agtgggggggtcagccccccgcccggccagccgccccatccgggaggtgaggggcgcttc -tgcccggccgcccctactgggaagtgaggagcccctctgcccggccacgaccccgtctgg -gaggtgtgcccagcggctcattggggatgggccatgatgacaatggcggttttgtggaat -agaaaggcgggaagggtggggaaaaaattgagaaatcggatggttgccgggtctgtgtgg -atggaagtagacat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b3eaf30d55b2199524601cef564f628f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b3eaf30d55b2199524601cef564f628f.msa deleted file mode 100644 index 16b1b58a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b3eaf30d55b2199524601cef564f628f.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:63048983-63049269 -ggtttatccaggaggagcccggggagaggggggtgggaaaagccacagttttggaggtca -gcaaggtcatgtgggggcagactcctcctcctcctcctcttcctcctcctcctcctcttc -ctcttcttcctcctcctcctcttcctcttcctcctcct---------------------- ------cctcctcttcctcctcctcctcctcttcctccccctcctcttcctcctcctcctc -ttccttctcctcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttc -ctcctcctcttcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctc -ttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttc -ctcttcctcctcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttc -ctcttcctcctcc---------------------------------------tcttcctc -tttctcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttc -ctcctcctcctcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttc -ctcttcctcttcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttc -ctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctc -ctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctc -ctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcc -tcctcctcttcctcctcctcctcttcctctcctcctcctcctcctc ->syndip_2_chr20:63048983-63049269 -ggtttatccaggaggagcccggggagaggggggtgggaaaagccacagttttggaggtca -gcaaggtcatgtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctc -ctcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttc -ctcctcctcctcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctc -ttcctcctcctcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttc -ctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttc -ctcttcctcctcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttc -ctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctc -cttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctc -ctcctcctcctcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctc -ttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctc -ctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctc -ctcctcttcctcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctc -ctcttcctcctcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcc -tcctcctcttcctcctcctcctcttcctctcctcctcctcctcctc ->p:HG002_1_chr20:63048983-63049269 -ggtttatccaggaggagcccggggagaggggggtgggaaaagccacagttttggaggtca -gcaaggtcatgtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctc -ctcctcctcttcctcttcctcctcctcctcctcttcctcttcctcctcctcctcctcttc -ctcctcctcctcttcctcctcctcctcttcctcctccccctcctcttcctcctcctcctc -ttcctcctcctcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttc -ctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcttcctccttctcttc -ctcttcctcctcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttc -ctcctcttcctcctcctcttcctcctcctcctcctcttcctcctcctcctcgtcttcctc -cttctcctcttcctcctcttcctcttcctcctcctcttcctcttcctcttcctcttcctc -ctcctcctcctcttcctcctcctcctcctcttcctcctcctcctcttcctcctcctcctc -ttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctcctcctcttcctc -ctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctcctcttcctcctc -ctcctcttcctcctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctc -ctcttcctcctcctcttcctcctcctcctcctcttcctcc-cctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcc -tcctcctcttcctcctcctcctcttcctctcctcctcctcctcctc ->p:HG002_2_chr20:63048983-63049269 -ggtttatccaggaggagcccggggagaggggggtgggaaaagccacagttttggaggtca -gcaaggtcatgtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctc -ctcctcctcttcctcttcctcctcctcctcctcttcct---------------------- ------cctcctcctcctcttcctcctcttcctcctccccctcctcttcctcctcctcctc -ttccttctcctcctccttctcctcctcctcttcctcctcttcctcttcctcctcctcttc -ctcctcctcttcctcctcctctttctcctcctcttcctcttcctcctcttcctcctcctc -ttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctccttctcttc -ctcttcctcctcctcttcctcttcctcctcctcttcctctttctcctcctcctcctcttc -ctcttcctcctcc---------------------------------------tcttcctc -tttctcctcctcctcctcttcctcctcttcctcctcctcttcctcctcctcctcctcttc -ctcctcctcctcgtcttcctccttctcctcttcctcctcttcctcttcctcctcctcttc -ctcttcctcttcctcttcctcttcctcctcctcctcctctttctcctcctcctcctcttc -ctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcttcctcctc -ctcctcttcctcctcttcttcctcctcttcctcctcctcctcttcctcctcttcctcctc -ctcttcctcctcctcctcttcctcctcctcctcttcctcctcctcctcttcctcctcctc -ctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctcttcctcccctcc -tcctcctcttcctcctcctcctcttcctctcctcctcctcctcctc ->ref_chr20:63048983-63049269 -ggtttatccaggaggagcccggggagaggggggtgggaaaagccacagttttggaggtca -gcaaggtcatgtgggggcagactcctcctcctcctcctcttcctcctcctcctcttcctc -ctcctcctcttcctcttcctcctcctcctcctcttcctcctcctcctcctcttcctc--- ------cctcctcttcctcctcctcctcttcctcctcctcttcctcctcctcctcctcttc -ctcc-cctcctcctcctcttcctcctcctcctcttcctc-tcctcctcctcctcctc--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b422101c521eb16adc9b18b906a2c4c0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b422101c521eb16adc9b18b906a2c4c0.msa deleted file mode 100644 index 5275f47a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b422101c521eb16adc9b18b906a2c4c0.msa +++ /dev/null @@ -1,150 +0,0 @@ ->syndip_1_chr20:64134782-64136487 -tagcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtcc -ccggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtcctt -gacagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacac -acgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacac -acacgctccctcagttttgtgcgtc----------------------------------- ---acacacacgctccctcagttttgtgcg------------------------------- ------------------------------------------------------------- ------------------------------------------ccacaaacacgcgcactcc -ctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaacacaca -cgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaa -cacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgctt -cacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagtttt -gtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagtt -ttgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccc -tcagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctc -cctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacat -tccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacac -acacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccc -aaacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaa -acacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcg -tcacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagt -tttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctca -gttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctcc -ctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgct -ccctcagttttgtgtg---------------------------------tcacaaacaca -cacgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggctt -gaagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattt -agccgttattgagggacatcgaggtt ->syndip_2_chr20:64134782-64136487 -tagcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtcc -ccggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtcctt -gacagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacac -acgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacac -acacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcac -aaacacagacgctccctcagttttgcgca------------------------------- ------------------------------------------------------------- ------------------------------------------tcacaaacacacacgctcc -ctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacaca -cgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaa -cacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgctt -cacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagtttt -gtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagtt -ttgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccc -tcagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctc -cctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacat -tccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacac -acacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccc -aaacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaa -acacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcg -tcacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagt -tttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctca -gttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctcc -ctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgct -ccctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacaca -cacgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggctt -gaagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattt -agccgttattgagggacatcgaggtt ->p:HG002_1_chr20:64134782-64136487 -tagcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtcc -ccggtgtgtgatgttccccttgaaaaggaagcgtttctgcttctcctctttccggtcctt -gacagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacac -acgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacac -acacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcac -aaacacagacgctccctcagttttgcgca------------------------------- ------------------------------------------------------------- ------------------------------------------tcacaaacacacacgctcc -ctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacaca -cgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaa -cacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgctt -cacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagtttt -gtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagtt -ttgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccc -tcagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctc -cctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacat -tccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacac -acacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccc -aaacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaa -acacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcg -tcacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagt -tttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctca -gttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctcc -ctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgct -ccctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacaca -cacgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggctt -gaagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattt -agccgttattgagggacatcgaggtt ->p:HG002_2_chr20:64134782-64136487 -tagcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtcc -ccggtgtgtgatgttccccttgaaaaggaagcgtttctgcttctcctctttccggtcctt -gacagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacac -acgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacac -acacgctccctcagttttgtgcgtc----------------------------------- ---acacacacgctccctcagttttgtgcg------------------------------- ------------------------------------------------------------- ------------------------------------------ccacaaacacgcgcactcc -ctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacaaacacaca -cgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaa -cacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgctt -cacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagtttt -gtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagtt -ttgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccc -tcagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctc -cctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacat -tccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacac -acacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccc -aaacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaa -acacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcg -tcacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagt -tttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctca -gttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctcc -ctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgct -ccctcagttttgtgtg---------------------------------tcacaaacaca -cacgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggctt -gaagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattt -agccgttattgagggacatcgaggtt ->ref_chr20:64134782-64136487 -tagcattaggtgtatctcctaatgctatccctcccctctccccgcaccccacaaaagtcc -ccggtgtgtgatgttccccttgaaaaggaggcgtttctgcttctcctctttccggtcctt -gacagtgattccgtgcatcacaaacacacacgctccctcagttacacgaatcacaaacac -acgctccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacac -acacgctccctcagttttgtgcgccacaaacacgcgcactccctcagttatgtgcgtcac -aaacacagacgctccctcagttttgcgcatcacaaacacacacgctccctcagttatgga -catcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctccctcagt -tatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacacacgctcc -ctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaacacaca -cgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgcttcacaaa -cacacacgctccctcagttatggacatcacaaacacacacgctccctcagttttgtgctt -cacaaacacacacgctccctcagttatggacatcacaaacacacacgctccctcagtttt -gtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgctccctcagtt -ttgtgtgtcacaaacacacacgctccttcagttttgtgcttcacaaacacacacgctccc -tcagttttgtgcatcacacacacattccctcagttttgtgcgccacaaacacgcgcgctc -cctcagttttgtgcatcacaaacgcacatgctccctcagttttgggcatcacaaacacat -tccctcagttttgtgcatcacaaacgcacacgctccctcagttttgtgcgtcacaaacac -acacgctacctcagttttgtgtgttacaaacacacacgctccctcagtttcgtgcatccc -aaacatgctccctcagttatgtgcgtcacaaacacgctccctcagttttgtgtgtcacaa -acacacacgctccctcagttttgtgcatcacaaacacacacattccctcagttttgtgcg -tcacaaacacgcgtgctctctcagttatgtgcgtcacaaacacagacgctccctcagttt -tgcgcatcacacacacgctccctcagctttgtgcttcacaaacacacacgctccctcagt -tttgtgtgttacaaacacacacgctccctcagtttcgtgcatcccaaagacgattcctca -gttttgtgcatcacaaacacatatgctccctcagttttgtgcgtcacaaacgcgcgctcc -ctcagttatgtgcgtcacaaacacagacgctccctcagttttgcgcatcacacacacgct -ccctcagttttgtgtgtcacaaacacacacgctccctcagttttgcgcatcacaaacaca -cacgctccctcagttgtcaggggactttgcactgtgcctttgcatgaaacaccatggctt -gaagaggtcccgcatcgttagggcccccttgcccatggtgtggcgtcccctgaccgattt -agccgttattgagggacatcgaggtt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b4b25fe75fa812465ce27c19d1fe0ff9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b4b25fe75fa812465ce27c19d1fe0ff9.msa deleted file mode 100644 index 2b529a23..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b4b25fe75fa812465ce27c19d1fe0ff9.msa +++ /dev/null @@ -1,225 +0,0 @@ ->syndip_1_chr20:56280322-56282214 -ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag -tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca -aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa -catccatatatagatatatctatatatctatctatagctac------------------- ----------------------------------------------atctacagatatcta -tagccacatctacagatatctatagctacatctacagatatctacagatatctacagcta -catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata -tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc -tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata -tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga -tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta -tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata -aatctatatagatatataaaatag------------------------ataaatctatat -agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat -ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat -aaatctatatagatatatatacataaatctatatagatatatatacataaatctatatag -atatatatacataaatctatatagatatatacataaatctatacagatacatatacataa -atctatacagatacatatacataaatctatacagatacatatacataaatctatacagat -atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac -agatatatagatacatatagatacatctatacagatatatagatacatatagatacatct -atacagatatatagatacatatagatacatctatacagatatatagatacatatagatac -atctatacagatatatagatacatatagatacatctatacagatatatagatacatatag -atacatctatacagatatatagatacatatagatacatctatacagatatattgatacat -atagatacatctatatagatatattgatacatatagatacatctatatagatatattgat -acatatagatacatctatatagatatattgatacatatagatacatctatatagattaga -tatatatagatacatctatatagattagatatatatagatacatctatatagattagata -tatatagatacatctatatatagatatatagatatatatagatacatctatatatagata -tatagatatatatagatacatctatatatagatatatagatgtatatagatacatctata -tatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagata -catctatatatagatatatagatgtatatagatacatctatatatagatatatagatgta -tatagatacatctatatatagatatatagatgtatatagatacatctatatatagatata -tagatgtatatagatacatctatatatagatatatagatgtatatagatacatctatata -tagatatatagatgtatatagatacatctatatatagatatatagatgtatatagataca -tagatatatatagatacatttatgtatatatatatgtatatatagatatatagatatata -tagatacatctacacagagagatatatagaaacatctacacagggagatatatagataca -tctacatagagagatatatagatacatctacatagagagatatatagatacatctacata -gagagatatatagatacatctacatagagagatatatagatacatctacatagagagata -tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata -catctacatagagagatatatagatacatctacatagagagatatatagatacatctaca -tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata -tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc -tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt -actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccc ->syndip_2_chr20:56280322-56282214 -ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag -tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca -aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa -catccatatatagatatatctatatatctatctatagctacatctacagatatctatagc -tacatctacagatatctacagatatctatagctacatctacagatatctacagatatcta -tagctacatctacagatatctatagctacatctacagatatctacagatatctacagcta -catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata -tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc -tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata -tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga -tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta -tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata -aatctatatagatatataaaatag------------------------ataaatctatat -agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat -ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat -aaatctatatagatatatatacataaatctatatag------------------------ ---atatatacataaatctatat--atatatacataaatctatatagatatatatacataa -atctatatagatacatatagataaatctatacaga------------------------t -atataaatatatatagataaatctatacagatatatagatacatatagataaatctatac -agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct -atacagatatatagatacatatagataaatctatacagatatatagatacatatagataa -atctatacagatatatagatacatatagataaatctatacagatatatagatacatatag -ataaatctatacagatatatagatacatatagataaatctatacagatatatagatacat -atagatacatctatatagatatattgatacatatagatacatctatatagatatatagat ---atatagatacatctata----------------------------------------- -------------------------------------------------------tagata -tatatagatacatctatatatagacatatagatatatatagatacatctatatatagata -tatagatatatatagatacatctatatatagatatatagat------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------atatatagatacatctacacagagagatatatagaaacatctacacagggagata -tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata -catctatatagagagatatatagatacatctatatagagagatatatagatacatctaca -tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata -tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc -tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt -actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccc ->p:HG002_1_chr20:56280322-56282214 -ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag -tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca -aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa -catccatatatagatatatctatatatctatctatagctacatctacagatatctatagc -tacatctacagatatctacagatatctatagctacatctacagatatctacagatatcta -tagctacatctacagatatctatagctacatctacagatatctacagatatctacagcta -catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata -tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc -tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata -tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga -tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta -tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata -aatctatatagatatataaaatag------------------------ataaatctatat -agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat -ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat -aaatctatatagatatatatacataaatctatatag------------------------ ---atatatacataaatctatat--atatatacataaatctatatagatatatatacataa -atctatatagatacatatagataaatctatacaga------------------------t -atataaatatatatagataaatctatacagatatatagatacatatagataaatctatac -agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct -atacagatatatagatacatatagataaatctatacagatatatagatacatatagataa -atctatacagatatatagatacatatagataaatctatacagatatatagatacatatag -ataaatctatacagatatatagatacatatagataaatctatacagatatatagatacat -atagatacatctatatagatatattgatacatatagatacatctatatagatatatagat ---atatagatacatctata----------------------------------------- -------------------------------------------------------tagata -tatatagatacatctatatatagacatatagatatatatagatacatctatatatagata -tatagatatatatagatacatctatatatagatatatagat------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------atatatagatacatctacacagagagatatatagaaacatctacacagggagata -tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata -catctatatagagagatatatagatacatctatatagagagatatatagatacatctaca -tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata -tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc -tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt -actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccc ->p:HG002_2_chr20:56280322-56282214 -ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag -tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca -aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa -catccatatatagatatatctatatatctatctatagctac------------------- ----------------------------------------------atctacagatatcta -tagccacatctacagatatctatagctacatctacagatatctacagatatctacagcta -catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata -tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc -tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata -tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga -tatatagagagaaacctatatagatatatagatatatagagataaacctatatagatgta -tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata -aatctatatagatatataaaatag------------------------ataaatctatat -agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat -ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat -aaatctatatagatatatatacataaatctatatagatatatatacataaatctatatag -atatatatacataaatctatatagatatatacataaatctatacagatacatatacataa -atctatacagatacatatacataaatctatacagatacatatacataaatctatacagat -atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac -agatatatagatacatatagatacatctatacagatatatagatacatatagatacatct -atacagatatatagatacatatagatacatctatacagatatatagatacatatagatac -atctatacagatatatagatacatatagatacatctatacagatatatagatacatatag -atacatctatacagatatatagatacatatagatacatctatacagatatattgatacat -atagatacatctatatagatatattgatacatatagatacatctatatagatatattgat -acatatagatacatctatatagatatattgatacatatagatacatctatatagattaga -tatatatagatacatctatatagattagatatatatagatacatctatatagattagata -tatatagatacatctatatatagatatatagatatatatagatacatctatatatagata -tatagatatatatagatacatctatatatagatatatagatgtatatagatacatctata -tatagatatatagatgtatatagatacatctatatatagatatatagatgtatatagata -catctatatatagatatatagatgtatatagatacatctatatatagatatatagatgta -tatagatacatctatatatagatatatagatgtatatagatacatctatatatagatata -tagatgtatatagatacatctatatatagatatatagatgtatatagatacatctatata -tagatatatagatgtatatagatacatctatatatagatatatagatgtatatagataca -tagatatatatagatacatttatgtatatatatatgtatatatagatatatagatatata -tagatacatctacacagagagatatatagaaacatctacacagggagatatatagataca -tctacatagagagatatatagatacatctacatagagagatatatagatacatctacata -gagagatatatagatacatctacatagagagatatatagatacatctacatagagagata -tatagatacatctacatagagagatatatagatacatctacatagagagatatatagata -catctacatagagagatatatagatacatctacatagagagatatatagatacatctaca -tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata -tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc -tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt -actctcgatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccc ->ref_chr20:56280322-56282214 -ggtggacatagtgtatctacagatgggacaatctaagatggttacaacattactacatag -tatcgcaaatagaaatggaaagcctgaatctaaccatgagaaaatttaaaataactatca -aaaaggtaacatccatatacagatataatatctataacatatatagatatatggatataa -catccatatatagatatatctatatatctatctatagctac------------------- --------------atctacagatatctatagctacatctacagatatctacagatatcta -tagctacatctacagatatctatagctacatctacagatatctacagatatctacagcta -catctacagatatctatagatatctatagctatatctacagatatctatcgatagatata -tctatcgatagatatatccacatagatatctagatatatatggatatatctatagatatc -tatctggatatatctatcgatagatatatagatatatatagataaagctatatagatata -tatagataaacctatatagatacatagatatatagagagaaacctatatacatatataga -tatatagagagaaacctatatagatatatagatatatagagagaaacctatatagatgta -tagataaacctatatagatatatagataaacctatgtagatatatagatatatatagata -aatctatatagatatataaaatagataaatctatatagatatatatacataaatctatat -agatatatatacataaatctatatagatatatatacataaatctatatatatacataaat -ctatatatacataaatctatatagatatatatacataaatctatatagatatatatacat -aaatctatatagatatatatacataaatctatatag------------------------ -atatatatacataaatctatatagatatatacataaatctatatagatatatatacataa -atctatatagatatatatacataaatctatatagatatatatacataaatc--------t -atatagatacatatagataaatctatacagatatatagatacatatagataaatctatac -agatatatagatacatatagataaatctatacagatatatagatacatatagataaatct -atacagatatatagatacatatagataaatctatacagatatatagatacatatagataa -atctatacagatatatagatacatatagataaatctatacagatatatagatacatatag -atacatctatacagatatatagatacatatagatacatctatacagatatatagatacat -atagatacatctatacagatatattgatacatatagatacatctatatagatatatagat ---atatagatacatctata----------------------------------------- -------------------------------------------------------tagata -tatagatata----tagatacatctatatagatatatatagatacatctatatatagaca -tatagatatatatagatacatctatatatagatatatagat------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------atatatagatacatctacacagagagatatatagaaacatctacacagggagata -tatagatacatctacacagagagatatatagatacatctac------------------- --------atagagagatatatagatacatctacatagagagatatatagatacatctaca -tagagagatatatagatacatctacatagagagatatatagatacatctacatagagata -tatatagatacatctacatagagatatatatagatacatctatatagagatatatctacc -tatacttcctgtgagttgtgtttctctggagaactaataggtagggtgactgtataattt -actctccatactgggacacttttaatcattgctataatacattaattttaatctaatctt -cttatccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b592bd7606102ee30703461d14728bdd.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b592bd7606102ee30703461d14728bdd.msa deleted file mode 100644 index 82b0e36d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b592bd7606102ee30703461d14728bdd.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:2240825-2241826 -gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg -agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat -cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt -tctctctctctccttccttccttctttccttccctccctcccttccttttttcttctttc -tttcattttctttctttctctctttcttctttctcttcctttcttc-------------- -----------------------------------------------tttcttttcctcct -tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc -tccctc-----------------------------------cttccctccctccctttct -ttctcctt-----------ttcttccttccctccctgcctgtctccctctttctttctct -tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc -ctcctccctctttttctttctttctttcttttttctttctctcttc-ttttttttttttt -tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact -gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga -ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg -gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc -agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct -taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattct ->syndip_2_chr20:2240825-2241826 -gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg -agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat -cttctcaaagttttctt-------------------tttctttctttctttttctttctt -tctctctctctccttccttccttctttccttccctccctcccttccttttttcttcttcc -tttcattttctttctttctctctttcttctttctcttcctttcttctttcttttcctcct -tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc -tccctccttccctccctccctttcttccttctttccttatccctcccttctttccttcct -tccctttgtttctctttctttctttctttctctctctcttccttccttccctccctccct -ccctccttcctcccttctttccttccctccctgcctctctgtctccctctttctttctct -tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc -ctcctccctctttttctttctttctttcttttttctctctctcttctttttttttttttt -tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact -gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga -ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg -gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc -agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct -taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattct ->p:HG002_1_chr20:2240825-2241826 -gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg -agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat -cttctcaaagttttctt-------------------tttctttctttctttttctttctt -tctctctctctccttccttccttctttccttccctccctcccttccttttttcttcttcc -tttcattttctttctttctctctttcttctttctcttcctttcttctttcttttcctcct -tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc -tccctccttccctccctccctttcttccttctttccttatccctcccttctttccttcct -tccctttgtttctctttctttctttctttctctctctcttccttccttccctccctccct -ccctccttcctcccttctttccttccctccctgcctctctgtctccctctttctttctct -tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc -ctcctccctctttttctttctttctttcttttttctctctctcttctttttttttttttt -tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact -gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga -ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg -gtcttgctatgttccccaggctagtctcaaactcctgggctcaagtgatcctccagcctc -agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct -taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattct ->p:HG002_2_chr20:2240825-2241826 -gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg -agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat -cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt -tctctctctctccttccttccttctttccttccctccctcccttccttttttcttctttc -tttcattttctttctttctctctttcttctttctcttcctttcttc-------------- -----------------------------------------------tttcttttcctcct -tcctcccttctttccttcccttccttcttccctccctccctctttgtttctttctttctc -tccctc-----------------------------------cttccctccctccctttct -ttctcctt-----------ttcttccttccctccctgcctgtctccctctttctttctct -tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc -ctcctccctctttttctttctttctttcttttttctttctctcttc-ttttttttttttt -tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact -gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga -ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg -gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc -agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct -taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattct ->ref_chr20:2240825-2241826 -gtgacccttaggtaaatcgttccaactctctgagcctcagtgttgttatctacaaatggg -agaatcaaggcaccctcctacaagcggcggctcatcagctcacttggaaaatgtagtcat -cttctcaaagttttctttttctttctttctttttcctttctttctttctttttctttctt -tctctctctctccttccttccttctttccttccctccctcccttccttttttcttctttc -tttcattttctttctttctctctttcttctttctcttcctttcttt-------------- --ccttccgtccctcccttccttccttttttcttcttcctttcat--tttctttctttctc -tctttcttctttctcttcctttcttctttcttttcctccttcctcccttctttccttccc -ttcctt-----------------------------------cttccctccctccctcttt -gtttctttctttctctccctccttccctccctccctttctgtctccctctttctttctct -tttttcttttccttccttccgtctttttcctcccttctttcctccctcctccctccctcc -ctcctccctctttttctttctttctttcttttttctttctctcttctttttttttttttt -tttttaagagatagggtctgttgcccaggctggagtgcagtggcatgatcatggttcact -gcagccttgaactcctgggctcaggtgatcctcctacctcagcctcctaagtagctggga -ctataggtgcatgccatcacacccagctaattttttaaaagaaattttgtaaagacaggg -gtcttgctatgttccccaggctggtctcaaactcctgggctcaagtgatcctccagcctc -agtatcccaaagtgctgggattataggtgtgagtcactgcagccagctcaaatattttct -taaatgaatgtaaggttgaggatgcattattataatggctaatttagatctaaaaaatgc -tttgcagtttaccagattcacttatgtacattct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b5c7108d4aa339a3fd1052ecc59f7f23.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b5c7108d4aa339a3fd1052ecc59f7f23.msa deleted file mode 100644 index c95d658a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b5c7108d4aa339a3fd1052ecc59f7f23.msa +++ /dev/null @@ -1,135 +0,0 @@ ->syndip_1_chr20:18209029-18210244 -tttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatct -ccccctattccagtcccccaggcatgtatccttccgtagcttctccacacctacacgaac -ctagacgattccttccacaccttccccacacccacacgaacctagacgattccttccaca -ccttccccacacccacacgaacctagatgaattccttccacaccttctccacacccacac -gaacctagacgattccttccacaccttccccacacccattctccacacccacacgaacct -agacgattccttccacacctccacacccacacgaacctagatgaattccttccacacctt -ccccacacccacacaaacctagacgattccttccacaccttctccacacccacacgaacc -tagacgaattccttccagaccttctccacacccacacagacctagacgattccttccaca -cctccacacccacacgaacctagacgaattccttccacaccttgtgcacacccacacgaa -cctagacgaattccttccacaccttctccacacccacacgaacctagacgaattccttcc -acaccttctccacacccacacgaacctagacgattccttccacactttccccacacccac -acgaacctagacg-attccttccacac---ctccacacccacacgaacctagatgaattc -cttccacaccttccccacacccacacaaacctagacgattccttccacaccttctccaca -cccacacaaacctagacaattccttccacacacacatgaacctagatgaattccttccac -accttctccacacccacatgaacctagacgattccttccacaccttctccacacccacac -acacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcct -tgcacaccttctccacacccacacgaacctagacgaattccttccacaccttctccatac -ccacacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaat -tccttccacaccttctccacacccacacgaacctaaacgattccttccacaccttctcca -cacccacacacacctagatgaattccttccacaccttccccacacccacacagacctaga -cgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacctt -ctccatacccacacgaacctagacaattccttccacaccttctcacacccacacaaacct -agatgaattccttccacaccttccccacacccacacagacctagacgaattccttccaca -ccttct-----------------------------------------ccacacccacacg -aacctagacaattccttgcacaccttctcacacccacacaaacctagacgaattccttcc -acaccttctccacacccacacaaacctagacgaattc ->syndip_2_chr20:18209029-18210244 -tttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatct -ccccctattccagtcccccaggcatgtatccttccgtagcttctccacacctacacgaac -ctagacgattccttccacaccttccccacacccacacgaacctagacgattccttccaca -ccttccccacacccacacgaacctagatgaattccttccacaccttctccacacccacac -gaacctagacgattccttccacaccttccccacacccattctccacacccacacgaacct -agacgattccttccacacctccacacccacacgaacctagatgaattccttccacacctt -ccccacacccacacaaacctagacgattccttccacaccttctccacacccacacgaacc -tagacgaattccttccagaccttctccacacccacacagacctagacgattccttccaca -cctccacacccacacgaacctagacgaattccttccacaccttgtgcacacccacacgaa -cctagacgaattccttccacaccttctccacacccacacgaacctagacgaattccttcc -acaccttctccacacccacacgaacctagacgattccttccacactttccccacacccac -aagaacctagacg-attccttccacac---ctccacacccacacgaacctagatgaattc -cttccacaccttccccacacccacacaaacctagacgattccttccacaccttctccaca -cccacacaaacctagacaattccttccacacacacatgaacctagatgaattccttccac -accttctccacacccacatgaacctagacgattccttccacaccttctccacacccacac -acacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcct -tgcacaccttctccacacccacacgaacctagacgaattccttccacaccttctccatac -ccacacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaat -tccttccacaccttctccacacccacacgaacctaaacgattccttccacaccttctcca -cacccacacacacctagatgaattccttccacaccttccccacacccacacagacctaga -cgaattccttccacaccttctccacacccacacgaacctagacgattccttccaca---- ---------ccacacgaacctagacaattccttccacaccttctcacacccacacaaacct -agatgaattccttccacaccttccccacacccacacagacctagacgaattccttccaca -ccttct-----------------------------------------ccacacccacacg -aacctagacaattccttgcacaccttctcacacccacacaaacctagacgaattccttcc -acaccttctccacacccacacaaacctagacgaattc ->p:HG002_1_chr20:18209029-18210244 -tttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatct -ccccctattccagtcccccaggcatgtatccttccgtagcttctccacacctacacgaac -ctagacgattccttccacaccttccccacacccacacgaacctagacgattccttccaca -ccttccccacacccacacgaacctagatgaattccttccacaccttctccacacccacac -gaacctagacgattccttccacaccttccccacacccattctccacacccacacgaacct -agacgattccttccacacctccacacccacacgaacctagatgaattccttccacacctt -ccccacacccacacaaacctagacgattccttccacaccttctccacacccacacgaacc -tagacgaattccttccagaccttctccacacccacacagacctagacgattccttccaca -cctccacacccacacgaacctagacgaattccttccacaccttgtgcacacccacacgaa -cctagacgaattccttccacaccttctccacacccacacgaacctagacgaattccttcc -acaccttctccacacccacacgaacctagacgattccttccacaccttccccacacccac -acagacctagacgaattccttgcacaccttctccacacccacacgaacctagacgaattc -cttccacaccttctccatacccacacgaacctagacaattccttccacaccttctccaca -cccacacaaacctagacaattccttccacacccacacaaacctagatgaattccttccac -accttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacac -acacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttctccacacccacacgaacctagacg-attccttccacaccttctccatac -ccacacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaat -tccttccacaccttctccacacccacacgaacctaaacgattccttccacaccttctcca -cacccacacacacctagatgaattccttccacaccttccccacacccacacagacctaga -cgaattccttccacaccttctccacacccacacgaacctagacgattccttccaca---- ---------ccacacgaacctagacaattccttccacaccttcccacacccacacagacct -agacgaattccttccacaccttctccacacccacacgaacctagacg-attccttccaca -ccttcc-----------------------------------------ccacacccacacg -aacctagacaattccttgcacaccttctcacacccacacaaacctagacgaattccttcc -acaccttctccacacccacacaaacctagacgaattc ->p:HG002_2_chr20:18209029-18210244 -tttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatct -ccccctattccagtcccccaggcatgtatccttccgtagcttctccacacctacacgaac -ctagacgattccttccacaccttccccacacccacacgaacctagacgattccttccaca -ccttccccacacccacacgaacctagatgaattccttccacaccttctccacacccacac -gaacctagacgattccttccacaccttccccacacccattctccacacccacacgaacct -agacgattccttccacacctccacacccacacgaacctagatgaattccttccacacctt -ccccacacccacacaaacctagacgattccttccacaccttctccacacccacacgaacc -tagacgaattccttccagaccttctccacacccacacagacctagacgattccttccaca -cctccacacccacacgaacctagacgaattccttccacaccttgtgcacacccacacgaa -cctagacgaattccttccacaccttctccacacccacacgaacctagacgaattccttcc -acaccttctccacacccacacgaacctagacgattccttccacactttccccacacccac -acgaacctagacg-attccttccacac---ctccacacccacacgaacctagatgaattc -cttccacaccttccccacacccacacaaacctagacgattccttccacaccttctccaca -cccacacaaacctagacaattccttccacacacacatgaacctagatgaattccttccac -accttctccacacccacatgaacctagacg------------------------------ -------------attccttccacaccttccccacacccacacagacctagacgaattcct -tgcacaccttctccacacccacacgaacctagacgaattccttccacaccttctccatac -ccacacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaat -tccttccacaccttctccacacccacacgaacctaaacgattccttccacaccttctcca -cacccacacacacctagatgaattccttccacaccttccccacacccacacagacctaga -cgaattccttccacaccttctccacacccacacgaacctagacgattccttccacacctt -ctccatacccacacgaacctagacaattccttccacaccttctcacacccacacaaacct -agatgaattccttccacaccttccccacacccacacagacctagacgaattccttccaca -ccttctccacacccacacgaacctagacgattccttccacaccttccccacacccacacg -aacctagacaattccttgcacaccttctcacacccacacaaacctagacgaattccttcc -acaccttctccacacccacacaaacctagacgaattc ->ref_chr20:18209029-18210244 -tttctgtgtttacagttatttccaaataaaaaataagcagaaaggaaaagctaatcatct -ccccctattccagtcccccaggcatgtatccttccgtagcttctccacacct-------- ----------------------------------acacgaacctagacgattccttccaca -ccttccccacacccacacgaacctagatgaattccttccacaccttctccacacccacac -gaacctagacgattccttccacaccttccccacacccattctccacacccacacgaacct -agacgattccttccacacctccacacccacacgaacctagatgaattccttccacacctt -ccccacacccacacaaacctagacgattccttccacaccttctccacacccacacgaacc -tagacgaattccttccagaccttctccacacccacacagacctagacgattccttccaca -cctccacacccacacgaacctagacgaattccttccacaccttgtgcacacccacacgaa -cctagacgaattccttccacaccttctccacacccacacgaacctagacgaattccttcc -acaccttctccacacccacacgaacctagacgattccttccacaccttccccacacccac -acagacctagacgaattccttgcacaccttctccacacccacacgaacctagacgaattc -cttccacaccttctccatacccacacgaacctagacaattccttccacaccttct----- ---------------------------cacacccacacaaacctagatgaattccttccac -accttctccacacccacacgaacctaaacgattccttccacaccttctccacacccacac -acacctagatgaattccttccacaccttccccacacccacacagacctagacgaattcct -tccacaccttctccacacccacacgaacctagacg-attccttccacaccttctccatac -ccacacgaacctagacaattccttccacaccttctcacacccacacaaacctagatgaat -tccttccacaccttccccacacccacacag------------------------------ ------------acctagacgaattccttccacaccttctccacacccacacgaacctaga -cg-attccttccacaccttccccacac--------------------------------- ---------ccacacgaacctagacaattccttgcacaccttctcacacccacacaaacct -agacgaattccttccacaccttctccacacccacacaaacctagacg------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------aattc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_b8963eabf50fbefd5fbf150779abc34d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_b8963eabf50fbefd5fbf150779abc34d.msa deleted file mode 100644 index c9333764..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_b8963eabf50fbefd5fbf150779abc34d.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:57189846-57190640 -ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg -gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta -cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc -acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg -ctggagaagtgagccaggaaccagagaggttgagactggagatagtgagcgaggaaccgg -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -c----agagtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccag -agggggtgaggctggagagagtgagccaggaaccagaggaggtgaggccaga----gtga -gtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg -ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaagg ->syndip_2_chr20:57189846-57190640 -ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg -gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta -cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc -acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg -ctggagaagtgagccaggaaccagaggggttgaggctggagatagtgagcgaggaaccgg -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg -aaggggtgaggctggagacagtgagcgaggaacca------------------------- ------------gagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg -ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaagg ->p:HG002_1_chr20:57189846-57190640 -ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg -gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta -cagggcagagtgagccatgggaggctttggggaggaaatgttcctggcagagggaatggc -acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg -ctggagaagtgagccaggaaccagaggggttgaggctggagatagtgagcgaggaaccgg -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg -aaggggtgaggctggagacagtgagcgaggaacca------------------------- ------------gagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg -ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaagg ->p:HG002_2_chr20:57189846-57190640 -ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg -gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta -cagggcagagtgagccatgggaggctttggggaggaaatgttcctggcagagggaatggc -acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg -ctggagaagtgagccaggaaccagagaggttgagactggagatagtgagcgaggaaccgg -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -c----agagtgagtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccag -agggggtgaggctggagagagtgagccaggaaccagaggaggtgaggccaga----gtga -gtgaggagcttgaaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg -ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaagg ->ref_chr20:57189846-57190640 -ctgggagctgactggcgagggagatcagctcaggggtgcacagtgctgtgtctgatggtg -gcaaggactaggaagaacctaggacagggtggcagggacatgacagtggggcacagtgta -cagggcagagtgagccatgggaggttttggggaggaaatgttcctggcagagggaatggc -acatgccaggttcatgagaaatacacggtgtgtgtcagcacagtgaagaggccagtgagg -ctggagaagtgagccaggaaccagagaggttgagactggagatagtgagcgaggaaccgg -agggggtgaagctggagagagtgagccaggaatcagaggaggtgaggccagagagagtga -gcgaggaaccagagggggtgaggctggagagagtgaccgaggaaccagaggaggtgaggc -tggagagagtgagccaggaaccagaggaggtgaggccag----agtgagtgaggagcttg -aaggggtgaggctggagacagtgagcgaggaaccagagggggtgaggctggagagcgtga -gtgaggagcccgagggggtgaggctggagagcgtgagtgaggagcccgagggggtgaggc -tggagagcgtgagtgaggagcccgagggggtgaggctggagagagtgagtgaggagccca -agggggtgaagccgaggtgggtatggggctgggtcacctggggtctcccagcccagtggg -ggatttgggcagggggcgacgtggccagggttctgtggtgggagacccattctgaatgcc -gtgtggggaaccaacaagg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bb633e8a0fe19e3e0ef87827050edb6d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bb633e8a0fe19e3e0ef87827050edb6d.msa deleted file mode 100644 index 5353344b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bb633e8a0fe19e3e0ef87827050edb6d.msa +++ /dev/null @@ -1,280 +0,0 @@ ->syndip_1_chr20:64125009-64128074 -attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt -ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc -tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt -ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc -tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct -tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc -aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta -ccaaagctttata-------------------------------ctcaaataccacactg -tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata -ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga -ttaccacagctttata-------------------------------ctcaaataccaca -ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct -tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca -aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac -cacagctgtatactcaaatact------------------------------------ac -accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt -tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc -aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta -ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc -acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct -ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt -cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac -tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat -taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat -actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact -gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat -actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa -atacc------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------acactgtcttgattaccacagctttatac -gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat -tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat -actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac -agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca -ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct -tgattaccac-------------------------------------------------- ------------------------------------------------------------- -----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac -tacactgtcttgattactac---------------------------------------- -------------------------------------agctttatactcaaatacc----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------acactgtcttgattact -atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga -ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt -ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tg ->syndip_2_chr20:64125009-64128074 -attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt -ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc -tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt -ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc -tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct -tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc -aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta -ccaaagctttata-------------------------------ctcaaataccacactg -tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata -ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga -ttaccacagctttata-------------------------------ctcaaataccaca -ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct -tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca -aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac -cacagctgtatactcaaatact------------------------------------ac -accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt -tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc -aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta -ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc -acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct -ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt -cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac -tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat -taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat -actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact -gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat -actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa -atacc------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------acactgtcttgattaccacagctttatac -gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat -tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat -actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac -agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca -ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct -tgattaccac-------------------------------------------------- ------------------------------------------------------------- -----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac -cacactgtcttgattactac---------------------------------------- -------------------------------------agctttatactcaaatacc----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------acactgtcttgattact -atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga -ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt -ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tg ->p:HG002_1_chr20:64125009-64128074 -attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt -ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc -tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt -ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc -tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct -tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc -aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta -ccaaagctttata-------------------------------ctcaaataccacactg -tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata -ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga -ttaccacagctttata-------------------------------ctcaaataccaca -ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct -tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca -aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac -cacagctgtatactcaaatact------------------------------------ac -accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt -tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc -aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta -ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc -acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct -ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt -cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac -tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat -taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat -actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact -gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat -actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa -atacc------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------acactgtcttgattaccacagctttatac -gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat -tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat -actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac -agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca -ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct -tgattaccac-------------------------------------------------- ------------------------------------------------------------- -----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac -cacactgtcttgattactac---------------------------------------- -------------------------------------agctttatactcaaatacc----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------acactgtcttgattact -atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga -ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt -ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tg ->p:HG002_2_chr20:64125009-64128074 -attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt -ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc -tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt -ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc -tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct -tgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactc -aaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatta -ccaaagctttata-------------------------------ctcaaataccacactg -tcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttata -ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga -ttaccacagctttata-------------------------------ctcaaataccaca -ctgtcttgattcctatagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct -tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca -aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac -cacagctgtatactcaaatact------------------------------------ac -accgtcttgattaccacagctgtatactcaaatactacactgtcttgattaccacagctt -tatactcaaataccacactgtcttgattaccaccgctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc -aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta -ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc -acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct -ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt -cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac -tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat -taccacagctttatactcaaataccacactgtcttgattactatagctttatactcaaat -actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact -gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat -actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa -atacc------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------acactgtcttgattaccacagctttatac -gcaaataccacactgtcttgattactatagctttatactcaaataccacactgtcttgat -tactacagctttatactcaaataccacactgtcttgattactacagctttatactcaaat -actacactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccac -agctttatactcaaatactacactgtcttgattactatagctttatactcaaataccaca -ctgtcttgattactatagctttatactcaaatactacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct -tgattaccac-------------------------------------------------- ------------------------------------------------------------- -----agctttatactcaaataccacactgtcttgattaccacagctttatactcaaatac -tacactgtcttgattactac---------------------------------------- -------------------------------------agctttatactcaaatacc----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------acactgtcttgattact -atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga -ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt -ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tg ->ref_chr20:64125009-64128074 -attacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgaggt -ttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggcc -tcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagtttt -ttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgcc -tggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatct -tgattactacagctt--------------------------------------tatactc -aaataccacaccgtcttgattaccacagctgtatactcaaataccacaccgtcttgatta -ccaaagctttatactcaaataccacactgtcttgattaccacagct-------------- ------------------ttatactcaaataacacaccgtcttgattaccacagctttata -ctcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttga -ttaccacagctttatactcaaatactacactgtcttgattcctatagc------------ --------------------tttatactcaaataccacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaatactacactgtct -tgattactatagctttatactcaaatactacactgtctgattactacagctttatactca -aataccaccctgtcttgattaccacagctttatactcaaataccacaccgtcttgattac -cacagctgtatactcaaatactactgtcctgattactacagctttatactcaaataccac -accgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccacagctt -tatactcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtc -ttgattactatagctttatactcaaatactacactgtctgattactacagctttatactc -aaataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta -ctatagctttatactcaaatactacactgtctgattactacagctttatactcaaatacc -acactatcttgattactacagctttatactcaaatactacactgtctgattactacagct -ttatactcaaataccacaccgtcttgattaccacagctttatactcaaatactacactgt -cttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatac -tcaaatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgat -taccacagctttatactcaaataacacactgtcttgattactatagctttatactcaaat -actacactgtctgattactacagctttatactcaaataccacactgtcttgattaccaca -gctttatactcaaatactacactgtctgattactacagctttatactcaaataccacact -gtcttgattaccacagctttatactcaaatactacactgtcttgattaccacagctttat -actcaaataccacaccgtcttgattaccacagctgtatactcaaataccacactgtcttg -attaccacagctgtatactcaaataccacactgtcttgattaccacagctttatactcaa -ataccacactgtcttgattactatagctttatactcaaataccacactgtcttgattacc -acagctttatacgcaaataccacactgtcttgattactatagctttatactcaaatacca -cactgtcttgattactacagctttatactcaaataccacactgtcttgattactacagct -ttatactcaaatactacactgtcttgattaacacagctttatactcaaatactacactgt -cttgattaccacagctttatactcaaatactacactgtcttgattactatagctttatac -tcaaataccacactgtcttgattactatagctttatactcaaatactacactgtcttgat -taccacagctttatactcaaatactacactgtcttgattact------------------ ---------------------atagctttatactcaaataccacactgtcttgattaccac ---------------------------------------agctttatactcaaataccaca -ctgtcttgattaccacagctttatactcaaataccacactgtcttgattaccacagcttt -atactcaaataccacactgtcttgattactatagctttatactcaaataccacactgtct -tgattactacagctttatactcaaataccacactgtcttgattaacacagctttatactc -aaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttgatta -ctatagctttatactcaaataccacactgtcttgattactatagctttatactcaaatac -tacactgtcttgattaccacagctttatactcaaatactacactgtcttgattactatag -ctttgtactcaaataccacactgtcttgattaccacagctttatactcaaataccacact -gtcttgattaccacagctttatactcaaataccacactgtcttgattactatagctttat -actcaaataccacactgtcttgattactacagctttatactcaaataccacactgtcttg -attactacagctttatactcaaatactacactgtcttgattaacacagctttatactcaa -atactacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaataccacactgtcttgattactatagctttatactctgttttga -ggtcaggtagtgtcagtccctctaacttcatttttcaaagttgttaggggattataggtt -ctttgcaaatttctatgcaaattttggaatcagtttgttaatttccagaaaaaagcctct -tg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bbc70dbaa5d67ccdda8d60a17b075dca.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bbc70dbaa5d67ccdda8d60a17b075dca.msa deleted file mode 100644 index 94768ca5..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bbc70dbaa5d67ccdda8d60a17b075dca.msa +++ /dev/null @@ -1,295 +0,0 @@ ->syndip_1_chr20:62057473-62059239 -tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg -gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga -cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc -aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg -gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag -gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc -tcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggc -tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca -cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag -acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa -tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc -aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac -ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg -ctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc -cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt -ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag -caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga -caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa -cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg -gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg -ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga -aggacg------------------------------------------------------ --------------------gacacaggtctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctc------------------------------------------------- -------------------------ggggggccaacctctccagtccccaaacacagtccc -caacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccctc -acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct -gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca -ggcctggagaagagcctgggaccaccgcggactgac ->syndip_2_chr20:62057473-62059239 -tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctc------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------ggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcgggggccaacctca-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------gcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa -cctcagcaagacctcaggaaggacggacacaggt-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga -aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag -caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctc------------------------------------------------- --------------------------gggggccaacctctccagtccccaaacacagtccc -caacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcctgccctc -acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct -gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca -ggcctggagaagagcctgggaccaccgcggactgac ->p:HG002_1_chr20:62057473-62059239 -tccaagatccatgtaccccaacaccaccctacctggccacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctc------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------ggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcgggggccaacctca-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------gcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa -cctcagcaagacctcaggaaggacggacacaggt-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga -aggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcag -caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctc------------------------------------------------- --------------------------gggggccaacctctccagtccccaaacacagtccc -caacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcctgccctc -acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct -gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca -ggcctggagaagagcctgggaccaccgcggactgac ->p:HG002_2_chr20:62057473-62059239 -tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctac -acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg -gacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaaga -cctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggcc -aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg -gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag -gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacc -tcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggc -tcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcca -cagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaag -acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaa -tggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacggac -acaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctc -aggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaac -ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg -ctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggc -cacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggt -ctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcaggaa -ggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctcag -caagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacaga -caatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctaca -caccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacgg -acacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa -cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg -gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg -ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag -gtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga -aggacg------------------------------------------------------ --------------------gacacaggtctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctc------------------------------------------------- -------------------------ggggggccaacctctccagtccccaaacacagtccc -caacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccctc -acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct -gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca -ggcctggagaagagcctgggaccaccgcggactgac ->ref_chr20:62057473-62059239 -tccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttgag -atcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggga -cacaaagggcccagcaagacctcaggaaggacggacacaggcctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcg--------------------------------- ------------------------------------------------------------- ------------------------------------------------------gggggcc -aacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatg -gggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacca -ggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcag -gaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacctc -agcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctc -gggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggg -ccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaa -tggggctcgggggccaacctca-------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------------------gcaagacc -tcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaa -cctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggg -gctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccagg -ccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacag -gcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagga -aggacg------------------------------------------------------ --------------------gacacaggtctacacaccaggccacagacaatggggctcgg -gggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacaga -caatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacac -accaggccacagacaatggggctcggggggccaacctctccagtccccaaacacagtccc -caacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccctc -acacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagct -gggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggca -ggcctggagaagagcctgggaccaccgcggactgac diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bc157131d3144d30768ee2a816502647.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bc157131d3144d30768ee2a816502647.msa deleted file mode 100644 index a3301a69..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bc157131d3144d30768ee2a816502647.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:55627528-55628415 -atatacatattgtatattacatatacataatacataaaatgtttaatacatacataatat -atacataatataatattgtatattattaaattatacatgtatatatgtatactatatgta -tatatgtatacaaaatatgtatataatatatacaaaaaatgtgtatttttgtacatatat -tgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatatattatg -taatataatatatacataatgtgtattacatacattatatgtaatatatacatatattat -ataatatatatgtatatat-tatataca------tatatattatatacatatatgtatat -attatatacatatatgtatatattatatattatgtatacacatatgtatatatgtatata -ttatatattatgtatacacatatgtatatatgtatatattatatattatgtatacatata -tgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatattatat -attatgtatacatatatgtatatatgtatatattatatattatgtatacatatatgtata -tatgtatatattatatattatgtatacatatatgtata---------------------- ------------------------------------------------------------- -------------------------------------------tatgtatacatgtatata -catatatacgtatacacatatatacgtg--------tatatacgtatatacacgtatata -ttaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggt -tttgtgtaatgcaaccaaataaatta ->syndip_2_chr20:55627528-55628415 -atatacatattgtatattacatatacataatacataaaatgtttaatacatacataatat -atacataatataatattgtatattattaaattatacatgtatatatgtatac-------- ----atgtatacaaaatatgtatataatatatacaaaaaatgtgtatttttgtacatatat -tgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatatattatg -taatataatatatacataatgtgtattacatacattatatgtaatatataca-----tat -atattatatacatatatatgtatatat--------------------tatatacatatat -attatatacatatatgtatatattatatattatgtatacacatatgtatatatgtatata -ttatatattatgtatacacatatgtatatatgtatatattatatattatgtatacac--- ------atatgtatatattatatattatgtatacacatatgtatatatgtatatattatat -attatgtatac--------atatatgtatatattatatattatgtatacatatatgtata -tatgtatatattatatattatgtatacatatatgtatatattatatattatgtatacata -tatgtatatattatatat------------------------------------------ -------------------------------------------tatgtatacatgtatata -catatatacgtatacacatatatacgtgtatatacatatatacgtatatacacgtatata -ttaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggt -tttgtgtaatgcaaccaaataaatta ->p:HG002_1_chr20:55627528-55628415 -atatacatattgtatattacatatacataatacataaaatgtttaatacatacataatat -atacataatataatattgtatattattaaattatacatgtatatatgtatac-------- ----atgtatacaaaatatgtatataatatatacaaaaaatgtgtatttttgtacatatat -tgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatatattatg -taatataatatatacataatgtgtattacatacattatatgtaatatataca-----tat -atattatatacatatatat-tatata---------------------catatatgtatat -attatatacatatatgtatatattatatattatgtatacacatatgtatatatgtatata -ttatatattatgtatacacatatgtatatatgtatatattatatattatgtatacac--- ------atatgtatatattatatattatgtatacacatatgtatatatgtatatattatat -attatgtatac--------atatatgtatatattatatattatgtatacatatatgtata -tatgtatatattatatattatgtatacatatatgtatatattatatattatgtatacata -tatgtatatattatatat------------------------------------------ -------------------------------------------tatgtatacatgtatata -catatatacgtatacacatatatacgtgtatatacatatatacgtatatacacgtatata -ttaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggt -tttgtgtaatgcaaccaaataaatta ->p:HG002_2_chr20:55627528-55628415 -atatacatattgtatattacatatacataatacataaaatgtttaatacatacataatat -atacataatataatattgtatattattaaattatacatgtatatatgtatactatatgta -tatatgtatacaaaatatgtatataatatatacaaaaaatgtgtatttttgtacatatat -tgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatatattatg -taatataatatatacataatgtgtattacatacattatatgtaatatataca-----tat -atattatatacatatatat-tatatacatatatgtatatattatatacatatatgtatat -attatatatatatatgtatatattatatattatgtatacatatatgtatatatgtatata -ttatatattatgtatacatatatgtatatatgtatatattatatattatgtatacatata -tgtatatatgtatacattatatattatgtatac------------------atattatat -attatgtatac--------atatatgtatatattatatattatgtatac--------ata -tatgtatatattatatattatgtatacatatatgtatatattatatattatgtatacata -tatgtatatat------------------------------------------------- ------------------------------------------gtatgtatacatgtatata -catatatacgtatacacatatatacgtg--------tatatacgtatatacacgtatata -ttaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggt -tttgtgtaatgcaaccaaataaatta ->ref_chr20:55627528-55628415 -atatacatattgtatattacatatacataatacataaaatgtttaatacatacataatat -atacataatataatattgtatattattaaattatacatgtatatatgtatac-------- ----atgtatacaaaatatgtatataatatatacaaaaaatgtgtatttttgtacatatat -tgtacaaaaatatgtatattatatatacaaaatatgtatataatatatacatatattatg -taatataatatatacataatgtgtattacatacattatatgtaatatataca-----tat -atattatatacatatatat-tatata---------------------catatatgtatat -attatatacatatatgtatatattatatattatgtatacacatatgtatatatgtatata -ttatatattatgtatacacatatgtatatatgtatatattatatattatgtatacacata -tgtatatatgtatatattatatattatgtatacacatatgtatatatgtatatattatat -attatgtatacatatatgtatatatgtatatattatatattatgtatacatatatgtata -tatgtatatattatatattatgtatacatatatgtatatattatatattatgtatacata -tatgtatatattatatattatgtatacatatatgtatatattatatattatgtatacata -tatgtatatattatatattatgtatacatatatgtatatatgtatgtatacatgtatata -catatatacgtatacacatatatacgtgtatatacatatatacgtatatacacgtatata -ttaaatgataaatttatatgtatatatgcgtgtgtgcacacacacacgagatatgttggt -tttgtgtaatgcaaccaaataaatta diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bd402172ece6674cf9fbe88768975d74.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bd402172ece6674cf9fbe88768975d74.msa deleted file mode 100644 index 32620fa1..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bd402172ece6674cf9fbe88768975d74.msa +++ /dev/null @@ -1,355 +0,0 @@ ->syndip_1_chr20:64173309-64176629 -cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc -ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac -cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc -cctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagttg -tgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccat -ttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctccc -tgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgacttc -tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcct -gcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcat -ctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggctt------------------------------------------ ---------------ctcctgcagcatctttccctgtagttgtgtccatttcccctccctg -gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg -cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattt -cccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctg -gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg -tagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc- ---tagttgtgtccatttcccctccctggctt----------------------------- ----------------------ctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgtagcaactttcctagttgtgtccatttcccctccctggcttct -cctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcc--------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------tagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgt -gtccattccccctccctggctt---ctcctgtagcatctttccctgtagttgtgtccatt -tcccctccctggcttctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagca -tctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggcgtctcctcctgcagcatctttcc---tagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcat -ctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccct -gtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagttg -tgtccatttcccctccctggcttctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgttcatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------ccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg -tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg ->syndip_2_chr20:64173309-64176629 -cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc -ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac -cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc -cctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagttg -tgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccat -ttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctccc -tgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgacttc -tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcct -gcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcat -ctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctg -gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg -cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttcc------------------ ------------------------------------------------------------- --------------------------tagttgtgtccatttcccctccctggcttctcctg -tagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggctt----------------------------- ----------------------ctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctacagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccatttcccctccctgg------cttctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgt -gtccatttcccctccctggctt---ctcctgtagcatctttcc----------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------tagttgtgtccat -ttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggcgtctcctcctgcagcatctttcc---tagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctc----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------ccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg -tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg ->p:HG002_1_chr20:64173309-64176629 -cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc -ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac -cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc -cctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagttg -tgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccat -ttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctccc -tgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgacttc -tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcct -gcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcat -ctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctg -gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg -cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgtagcatctttcc------------------ ------------------------------------------------------------- --------------------------tagttgtgtccatttcccctccctggcttctcctg -tagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggctt----------------------------- ----------------------ctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctacagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgta -gcatctttccctgtagttgtgtccatttcccctccctgg------cttctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgt -gtccatttcccctccctggctt---ctcctgtagcatctttcc----------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------tagttgtgtccat -ttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggcgtctcctcctgcagcatctttcc---tagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctc----- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------ccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg -tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg ->p:HG002_2_chr20:64173309-64176629 -cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc -ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac -cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc -cctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagttg -tgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtccat -ttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctccc -tgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgacttc -tcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcct -gcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcat -ctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggctt------------------------------------------ ---------------ctcctgcagcatctttccctgtagttgtgtccatttcccctccctg -gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg -cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccattt -cccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctg -gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg -tagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc- ---tagttgtgtccatttcccctccctggctt----------------------------- ----------------------ctcctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgtagcaactttcctagttgtgtccatttcccctccctggcttct -cctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttcc--------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------tagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgt -gtccattccccctccctggctt---ctcctgtagcatctttccctgtagttgtgtccatt -tcccctccctggcttctgcagcatctttccctgtagttgtgtccatttcccctccctggc -ttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagca -tctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---tag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggcgtctcctcctgcagcatctttcc---tagttgtgtccatttcccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttc -tcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcat -ctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccct -gtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagttg -tgtccatttcccctccctggcttctgcagcatctttccctgtagttgtgtccatttcccc -tccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgttcatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------ccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg -tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg ->ref_chr20:64173309-64176629 -cagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctcc -ccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccatac -cccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatccttc -cctt--------------------------------------------------tagttg -tgtccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtccat -ttcccctccctgacttctcctcctgcagcatctttcctagttgtgtccatttcccctccc -tgacttctcctcctgcag------------------------------------------ ------------------------------------------------------------- -----catctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagcat -ctttccttgtagttgtgtccatttcccctccctgacttctc------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------ctcctgcagcatccttccctgtagttgtgtccatttcccctccctg -gcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctg -cagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatcttt -ccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctg----- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------tagttgtgtccattccccctccctggcttctcctg -tagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtcc -atttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccattcccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccct -gacttctc--------------------------------------------ctcctgca -gcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgt -gtccatttcccctccctggcttctcctcctgcagcatctttcc----------------- -------------------------------ctgtagttgtgtccattccccctccctggc -ttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagca -tctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccat -tccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccct -ccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt- ---ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc---ct -gtagcatctttcc---tagttgtgtccatttcccctccctggctt---ctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctggctt---ctcctgtagcatctttccc -tgtagttgtgtccattccccctccctgacttctcctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttcc------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccct -gtagttgtgtccattc-------------------------------------------- ---------------------------------------------------------cccc -tccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctc -ctgtagcatctttcc--------------------------------------------- ---------tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttcc---tagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccattccccctccctggcgtctcctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgt -ccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccc -tccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgg -cttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcc -tcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctgg -tagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggtg -tggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_be5cb2eaeb7a6c82acffb2b381c6dd01.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_be5cb2eaeb7a6c82acffb2b381c6dd01.msa deleted file mode 100644 index bc28ff0f..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_be5cb2eaeb7a6c82acffb2b381c6dd01.msa +++ /dev/null @@ -1,35 +0,0 @@ ->syndip_1_chr20:24681956-24682235 -tgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatgcagcagga -ggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtgcggggtcca -cccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtttacc -caggaaactgtgaagtatctctctggcctttgtgaatcacca------------------ ------------------------------------------------------------- --------------------------------------- ->syndip_2_chr20:24681956-24682235 -tgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatgcagcagga -ggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtgaggggtcta -cccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcaggggtccacc -caggaaactgtgaagtacctctgtggcctttgtgaattaccacagtcaggggtccaccca -ggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtttacccagg -aaactgtgaagtatctctctggcctttgtgaatcacca ->p:HG002_1_chr20:24681956-24682235 -tgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatgcagcagga -ggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtgcggggtcca -cccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcaggggtccacc -caggaaactgtgaagtacctctgtggcctttgtgaattaccacagtcaggggtccaccca -ggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtttacccagg -aaactgtgaagtatctctctggcctttgtgaatcacca ->p:HG002_2_chr20:24681956-24682235 -tgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatgcagcagga -ggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtgcggggtcca -cccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtttacc -caggaaactgtgaagtatctctctggcctttgtgaatcacca------------------ ------------------------------------------------------------- --------------------------------------- ->ref_chr20:24681956-24682235 -tgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatgcagcagga -ggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtgcggggtcca -cccaggaaactgtgaagtacctctgtggcctttgtgaattaccacagtcaggggtccacc -caggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtttaccca -ggaaactgtgaagtatctctctggcctttgtgaatcacca-------------------- --------------------------------------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_bf3c6d0e1e84d3ccc658d28e7f12e2aa.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_bf3c6d0e1e84d3ccc658d28e7f12e2aa.msa deleted file mode 100644 index beb105bd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_bf3c6d0e1e84d3ccc658d28e7f12e2aa.msa +++ /dev/null @@ -1,155 +0,0 @@ ->syndip_1_chr20:14861836-14862842 -ggctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatgg -tattatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaatagga -cattggaggttttatatataaatatatatatatatttatatatatatttatatatatata -tatttatatatatttatatatatatttatatatatatttatatatatatttatatatata -tttatatatatatttatatatatatttatatatatatttatatatatatttatatatatt -tatatatatttatatatatttttatatatttttatatatataaatatataaaaatatata -taaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaa -tatatataaatatatatttatatataaatatatataaatatatatttatacataaatata -tataaatatatatttatacataaatatataaatatatataatatatataaatatatatta -tacataaatatataaatatatattatacataaatatataaatatatataaatatatataa -atatatatttatacataaatatataaatatatatataaatatatataaatatatataaat -atatatataaatatatatataaatatatataaatatatatataaatatatatataaatat -atataaatatatataaatatatatataaatatatataaatatatataaatatatatttat -atattaatatataaatatatataaatatatatttatatattaatatataaatatatatat -attaatatatataaatatatataaatatatatttatatattaatatatatatattaatat -atatatatttatatattaatatatatatttatatattaatatatataaatatattactat -gtatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaat -atatattaatatataaaatatatatataaatataaataaatatatatataaatatatata -aataaatatatatataaatatatataaataaatatataaatatatataaatatatatata -aatatatataaatatatataaatatatataaaaatatatataaatatatatataaatata -tataaatatatatataaatatatatataaatatatatataaatatatataaatatatata -taaatatatataaatatatatataattatatataaatatatataaatatatataaatata -tatataaatatatataaatatatataaatatatataaatatatatataaatatatataaa -tatatatatataaatatatataaatatatatataaatatatataaatatatatatataaa -tatatataaatatatatataaatatatataaatatatatataaatataaatatatatgta -taaatatatatataaatataaatatatatgtataaatatatatataaatatatatatata -aatatatatatacatatataaatatatatataaatatatataaaaatatatatatatata -tttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcc -ttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagc -agaag ->syndip_2_chr20:14861836-14862842 -ggctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatgg -tattatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaatagga -cattggaggttttatatataaatatatatatatatatttatatatatatttatatatata -tatttatatatatt---------------------------------------------- -----------------tatatatatttatatatatatttttatatatatttatatatatt ---tatatatttatatatatttatatatatttttatatatataaatatataaaa------- ------------------------------------------------------------- ------------------------------atatataaatatatataaatatataaatata -tataaatatatatttatacataaatatataaatatatataatatatataaatatatatta -tacataaatatataaatatatattatacataaatatataaatatatataaatatatataa -atatatatttatacataaatatataaatatat------atatatataaatatatataa-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------atatatatttatatattaatatatataaatatattactat -gtatatttatatatatttatataa--atatataaatatatgtaaatatatatataaaaat -atatattaatatataaaa---------atatatatataaatatatatataaatatatata -aataaatatatataaatatatatataaat--atatataaatatatataaatatatatata -aatatatataaatatatataaatatatatataaatatatatataaatatatataaatata -tataaataaatatataaatatatatataaatatatataaatatatatataaatatatata -aatatatatataaatatatataaatatatatataaatatatataaat--------atata -tataaatatatatataaatatatataaatatatataaatatatatatataaatatatata -aatatatatataaatataaatatatataaatatataaaaatatatatataaatataaata -tatataaatatatatgtataaatatatatataaatataaatatatataaatatatatata -taaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaa -tatatatataaatatatataaatatatatataaatatatataaaaatatatatatatttt -tttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcc -ttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagc -agaag ->p:HG002_1_chr20:14861836-14862842 -ggctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatgg -tattatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaatagga -cattggaggttttatatataaatatatatatatatatttatatatatatttatatatata -tatttatatatatt---------------------------------------------- -----------------tatatatatttatatatatatttttatatatatttatatatatt ---tatatatttatatatatttatatatatttttatatatataaatatataaaa------- ------------------------------------------------------------- ------------------------------atatataaatatatataaatatataaatata -tataaatatatatttatacataaatatataaatatatataatatatataaatatatatta -tacataaatatataaatatatattatacataaatatataaatatatataaatatatataa -atatatatttatacataaatatataaatatat------atatatataaatatatataa-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------atatatatttatatattaatatatataaatatattactat -gtatatttatatatatttatataa--atatataaatatatgtaaatatatatataaaaat -atatattaatatataaaa---------atatatatataaatatatatataaatatatata -aataaatatatataaatatatatataaat--atatataaatatatataaatatatatata -aatatatataaatatatataaatatatatataaatatatatataaatatatataaatata -tataaataaatatataaatatatatataaatatatataaatatatatataaatatatata -aatatatatataaatatatataaatatatatataaatatatataaat--------atata -tataaatatatatataaatatatataaatatatataaatatatatatataaatatatata -aatatatatataaatataaatatatataaatatataaaaatatatatataaatataaata -tatataaatatatatgtataaatatatatataaatataaatatatataaatatatatata -taaatatatatataaatatatataaatatatataaaaatatatataaatatatatataaa -tatatatataaatatatataaatatatatataaatatatataaaaatatatatatatttt -tttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcc -ttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagc -agaag ->p:HG002_2_chr20:14861836-14862842 -ggctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatgg -tattatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaatagga -cattggaggttttatatataaatatatatatatatttatatatatatttatatatatata -tatttatatatatttatatatatatttatatatatatttatatatatatttatatatata -tttatatatatatttatatatatatttatatatatatttatatatatatttatatatatt -tatatatatttatatatatttttatatatttttatatatataaatatataaaaatatata -taaatatataaaaatatataaaaatatataaatatatataaatatataaatatatataaa -tatatataaatatatatttatatataaatatatataaatatatatttatacataaatata -tataaatatatatttatacataaatatataaatatatataatatatataaatatatatta -tacataaatatataaatatatattatacataaatatataaatatatataaatatatataa -atatatatttatacataaatatataaatatatatataaatatatataaatatatataaat -atatatataaatatatatataaatatatataaatatatatataaatatatatataaatat -atataaatatatataaatatatatataaatatatataaatatatataaatatatatttat -atattaatatataaatatatataaatatatatttatatattaatatataaatatatatat -attaatatatataaatatatataaatatatatttatatattaatatatatatattaatat -atatatatttatatattaatatatatatttatatattaatatatataaatatattactat -gtatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaat -atatattaatatataaaatatatatataaatataaataaatatatatataaatatatata -aataaatatatatataaatatatataaataaatatataaatatatataaatatatatata -aatatatataaatatatataaatatatataaaaatatatataaatatatatataaatata -tataaatatatatataaatatatatataaatatatatataaatatatataaatatatata -taaatatatataaatatatatataattatatataaatatatataaatatatataaatata -tatataaatatatataaatatatataaatatatataaatatatatataaatatatataaa -tatatatatataaatatatataaatatatatataaatatatataaatatatatatataaa -tatatataaatatatatataaatatatataaatatatatataaatataaatatatatgta -taaatatatatataaatataaatatatatgtataaatatatatataaatatatatatata -aatatatatatacatatataaatatatatataaatatatataaaaatatatatatatata -tttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcc -ttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagc -agaag ->ref_chr20:14861836-14862842 -ggctctcctgctgctggccaagcaggaccccaaggtccactgggatgtacatacttatgg -tattatgctctgcaatacttgtgggggctgtggaatgcacacttccaaagtgaaatagga -cattggaggttttatatataaatatatatatatatatttatatatatatttatatatata -tatttatatatatt---------------------------------------------- -----------------tatatatatttatatatatatttatat----------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------atatataaatatatataaatatataaatata -tataaatatatatttatacataaatatataaatatata---------------------- ------atatatataaatatatattatacataaatatataaatatatataaatatatataa -atatatatttatacataaatatataaatatat------atatatataaatatatataa-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------atatatatttatatattaatatatataaatatattactat -gtatatttatatatatttatataaatatatataaatatatgtaaatatatatataaaaat -atatattaatatataaaa---------atatatat------------------------- --ataaatatatataaatatatatataaat--atatataaat------------------- ------------------------------------------------------------- ----------------------------------------atatatatataaatatatata -aatatatatataaatatatataaatatatatataaatatatataaat--------atata -tatataaatatatataa----------------------atatatatataaatatatata -aatatatatataaatataaatatatataaatatataaaaatatatatataaatataaata -tatataaatatatatgtataaatatatatataaatataaatatatataaatatatatata -taaatatatatataaat------------------------------atatatatataaa -tatatatataaatatatataaatatatatataaatatatataaatatatatatatatatt -tttttttaatagagaggatgaagaccaaagcagtgagttccacctaagctggcccttgcc -ttttgtctaacaggaaacccagtccttcctaatgggcacagaattttcagagaagagagc -agaag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c00504a27ac55beec570218a4eedf56f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c00504a27ac55beec570218a4eedf56f.msa deleted file mode 100644 index 9a20f373..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c00504a27ac55beec570218a4eedf56f.msa +++ /dev/null @@ -1,45 +0,0 @@ ->syndip_1_chr20:60702842-60703215 -tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc -acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac -atttgtcattgtctttctttcttttctttctctctctctctttcttttccttctttcttt -ctttctttctttctttctttctttctttctttctttctttctttcttttctttccttctt -ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt -ctttctttctttctttcttctttctttctttttctttcttttttttttgggatggagtct -cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct ->syndip_2_chr20:60702842-60703215 -tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc -acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac -atttgtcattgtctttctttcttttctttctctctctctctctctttcttttccttcttt -ctttctttctttctttctttcttcctttctttctttctttctttctttctttctttcttt -ctttct---tttctttccttctttctttctttctttc----------------------- ----------------------------------------tttttttttgggatggagtct -cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct ->p:HG002_1_chr20:60702842-60703215 -tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc -acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac -atttgtcattgtctttctttcttttctttctctctctctctctctttcttttccttcttt -ctttctttctttctttctttcttcctttctttctttctttctttctttctttctttcttt -ctttct---tttctttccttctttctttctttctttc----------------------- ----------------------------------------tttttttttgggatggagtct -cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaacctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct ->p:HG002_2_chr20:60702842-60703215 -tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc -acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac -atttgtcattgtctttctttcttttctttctctctctctctttcttttccttctttcttt -ctttctttctttctttctttctttctttctttctttctttctttcttttctttccttctt -ctttctttctttctttctttctttctttctttctttctttctttctttctttctttcttt -ctttctttctttctttcttctttctttctttttctttcttttttttttgggatggagtct -cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaacctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct ->ref_chr20:60702842-60703215 -tatggtaactgcatgttgactcttttgaggagcttccagactgtttttcaaagtgatggc -acaattttcctttcccctcaataatgtatgagggttgcaatgtcgctacatattaccaac -atttgtcattgtctttctttcttttctttctctctctctctttct--------------- --------------tttccttctttctttctttctttctttctttctttctttctttcttt -cttttc---tttccttctttctttctttctttctttc----------------------- ----------------------------------------tttttttttgggatggagtct -cgctctgtcacccaggctggagtgcagtggcatgatctcggctcgctgcaatctccacct -cccaggttcaagcgattgaactcactgcctcagcctcccaagtagct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c09854a1826e6b88567130408713a7f9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c09854a1826e6b88567130408713a7f9.msa deleted file mode 100644 index c0ef88d2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c09854a1826e6b88567130408713a7f9.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:24681888-24682377 -ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag -ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg -cagcaggaggcaaactgtgaagtacctctctggc-------------------------- ------------------------------------------------------------- -------------------------------ctggcctttgtgaattaccacagtgcgggg -tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt -tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta -tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc -agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga -ggaggaga ->syndip_2_chr20:24681888-24682377 -ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag -ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg -cagcaggaggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtca -ggggtctacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcagg -ggtccacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcagggg -tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt -tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta -tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc -agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga -ggaggaga ->p:HG002_1_chr20:24681888-24682377 -ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag -ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg -cagcaggaggcaaactgtgaagtacctctctggcctggcctttgtgaattaccacagtca -ggggtccacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcagg -ggtccacccaggaaactgtgaagtacctctctggcctttgtgaattaccacagtcagggg -tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt -tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta -tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc -agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga -ggaggaga ->p:HG002_2_chr20:24681888-24682377 -ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag -ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg -cagcaggaggcaaactgtgaagtacctctctggc-------------------------- ------------------------------------------------------------- -------------------------------ctggcctttgtgaattaccacagtgcgggg -tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt -tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta -tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc -agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctctga -ggaggaga ->ref_chr20:24681888-24682377 -ctctgctgctggggtgtactcgatgtcctggctcgactgacacagtcctgatcttgccag -ttggtgtctgtggacctgtgttttggcatggacaggcacaaggctaaggaggtcagcatg -cagcaggaggcaaactgtgaagtacctctctggc-------------------------- ---------------------------------ctggcctttgtgaattaccacagtgcgg -ggtccacccaggaaactgtgaagtacctctgtggcctttgtgaattaccacagtcagggg -tccacccaggaaactgtgaagtacctctctgggcgttgtgaattaccacagttaggggtt -tacccaggaaactgtgaagtatctctctggcctttgtgaatcaccacagttaggggtcta -tgcaggagtactggtcattcacagactcagctcattccaggccttagcagtgtgcacctc -agagtgaagcagagaggccccaggagaagccatggccacgccctcaacctcctgctccga -ggaggaga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c2337c7a32652e58e95d2d00738ba7cf.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c2337c7a32652e58e95d2d00738ba7cf.msa deleted file mode 100644 index 8d3070d2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c2337c7a32652e58e95d2d00738ba7cf.msa +++ /dev/null @@ -1,105 +0,0 @@ ->syndip_1_chr20:62875071-62875657 -gaactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaaga -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagccccgcaccctcacctgcaccctcacccccacccccacccccaccccca -cccccacccccacccgcacccccacccccacccgcacccccacccccacccccacccgca -cccccacccccacccccacccgcacccccacccccacccgcacccccacccccaccccca -cccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgca -cccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccgca -cccgcacccccacccccaccctcacccgcacccgcacccccacccccacccccacccgca -cccgcacccccacccccacccc------------cacccccacccccacccgcacccgca -cccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgcaccccca -cccgcacccccacccccacccccacccccacccgcacccgcacccccacccccaccccca -cccccacccccacccccacccccacccccaccctcacccgcacccccaccctcaccccca -ccctcacccccaccctcacccgcaccctcacccgcacccgcacccccaccct------ca -cccacaccctcacccccaccctcacccccacccccaccctcacccgcacccgcaccccca -ccctcacccccacccccacccccaccctcaccctcaccctcacccgcacccgcaccccca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacacc -cacatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaac -tgctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcggga -gctatcctgcc ->syndip_2_chr20:62875071-62875657 -gaactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaaga -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagccccgcaccctcacctgcaccctcacccccacccccacccccaccccca -cccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgca -cccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgca -cccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcaccccca -cccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgca -cccccacccccacccccacccgcacccccacccccacccccacccgcacccgcaccccca -cccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcaccccca -cccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgca -cccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgca -cccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcaccccca -ccctcacccccaccctcacccgcacccccacccccacccccacccccaccctccccccca -cccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcaccccca -ccctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacacc -cacatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaac -tgctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcggga -gctatcctgcc ->p:HG002_1_chr20:62875071-62875657 -gaactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaaga -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagccccgcaccctcacctgcaccctcacccccacccccacccccaccccca -cccccacccgcacccgcacccccacccccacccgcacccccacccccacccccacccgca -cccccacccccacccccacccgcacccccacccccacccccacccgcacccgcacccgca -cccccacccccacccgcacccccacccccacccgcacccgcacccccacccgcaccccca -cccccacccccaccctcacccccacccgcacccccacccccacccccacccgcacccgca -cccccacccccacccccacccgcacccccacccccacccccacccgcacccgcaccccca -cccgcacccccacccccacccccacccgcacccgcacccccacccgcacccgcaccccca -cccgcacccccacccccacctccacccccacccgcacccgcacccccacccccacccgca -cccccacccccacccgcacccccacccccaccctcacccgcacccccacccccacccgca -cccccacccccaccctcacccccaccctcacccgcacccgcacccccaccctcaccccca -ccctcacccccaccctcacccgcacccccacccccacccccacccccaccctccccccca -cccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcaccccca -ccctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacacc -cacatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaac -tgctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcggga -gctatcctgcc ->p:HG002_2_chr20:62875071-62875657 -gaactttcctggcacactggagaggacggcagaacgctggaatggatttatcgtgcaaga -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagccccgcaccctcacctgcaccctcacccccacccccacccccaccccca -cccccacccccacccgcacccccacccccacccgcacccccacccccacccccacccgca -cccccacccccacccccacccgcacccccacccccacccgcacccccacccccaccccca -cccgcacccccacccccacccccacccgcacccgcacccccacccccacccgcacccgca -cccccacccccacccccacccgcacccccacccccacccccacccccacccgcacccgca -cccgcacccccacccccaccctcacccgcacccgcacccccacccccacccccacccgca -cccgcacccccacccccacccc------------cacccccacccccacccgcacccgca -cccgcacccccaccctcaccctcacccgcacccgcacccccacccccacccgcaccccca -cccgcacccccacccccacccccacccccacccgcacccgcacccccacccccaccccca -cccccacccccacccccacccccacccccaccctcacccgcacccccaccctcaccccca -ccctcacccccaccctcacccgcaccctcacccgcacccgcacccccaccct------ca -cccacaccctcacccccaccctcacccccacccccaccctcacccgcacccgcaccccca -ccctcacccccacccccacccccaccctcaccctcaccctcacccgcacccgcaccccca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacacc -cacatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaac -tgctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcggga -gctatcctgcc ->ref_chr20:62875071-62875657 -gaactttcctggcacactggagaggacggcagaacgctgggatggatttatcgtgcaaga -ccagcttgatgtccttagggcttggaggtcaccccttcacgaggattgtgaggagtgaat -tcatcggggagc------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------cccgcaccctcacctgcaccctca -cccccacccccacccccacccccacccccacccgcacccccacccccaccctccccccca -cccgcacccgcacccccaccctcacccgcacccccaccctcacccccaccctcaccccca -ccctcacccccacccccaccctcacccgcacccccactcgcacccgcacccccaccctca -cccgcacccccaccctcacccccaccctcacccccaccctcacccccacccccaccctca -cccgcaccctcactcgcaccgcaccctcactggcaccctcacccacaccgcacccacacc -cacatcggggaagagctccatgatcattcttttctgtaggcgaaaaactgcggcgggaac -tgctgccatgcagctgggctcccaatgcagtggggatggtggcgctctgggctggcggga -gctatcctgcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c78d05371e27551aac3ee432c6d3e724.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c78d05371e27551aac3ee432c6d3e724.msa deleted file mode 100644 index 9671f5ff..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c78d05371e27551aac3ee432c6d3e724.msa +++ /dev/null @@ -1,355 +0,0 @@ ->syndip_1_chr20:64173308-64176630 -acagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctc -cccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccata -ccccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatcctt -ccctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagtt -gtgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtcca -tttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctcc -ctgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgactt -ctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagca -tctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggctt----------------------------------------- ----------------ctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc ----tagttgtgtccatttcccctccctggctt---------------------------- -----------------------ctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgtagcaactttcctagttgtgtccatttcccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttcc-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------tagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttg -tgtccattccccctccctggctt---ctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggcttctgcagcatctttccctgtagttgtgtccatttcccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---ta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -tttcccctccctggcgtctcctcctgcagcatctttcc---tagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagca -tctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctc -cctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccc -tgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgtagcatctttccctgtagttgtgttcatttcccctc -cctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------ccatttcccctccctggcttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctg -gtagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggt -gtggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga ->syndip_2_chr20:64173308-64176630 -acagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctc -cccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccata -ccccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatcctt -ccctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagtt -gtgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtcca -tttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctcc -ctgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgactt -ctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagca -tctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgtagcatctttcc----------------- ------------------------------------------------------------- ---------------------------tagttgtgtccatttcccctccctggcttctcct -gtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggctt---------------------------- -----------------------ctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctacagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgt -agcatctttccctgtagttgtgtccatttcccctccctgg------cttctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttg -tgtccatttcccctccctggctt---ctcctgtagcatctttcc---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------tagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -tttcccctccctggcgtctcctcctgcagcatctttcc---tagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctc---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------ccatttcccctccctggcttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctg -gtagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggt -gtggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga ->p:HG002_1_chr20:64173308-64176630 -acagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctc -cccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccata -ccccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatcctt -ccctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagtt -gtgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtcca -tttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctcc -ctgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgactt -ctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagca -tctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgtagcatctttcc----------------- ------------------------------------------------------------- ---------------------------tagttgtgtccatttcccctccctggcttctcct -gtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggctt---------------------------- -----------------------ctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctacagcatctttccctgtagttgtgtccatttcccctccc -tggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgt -agcatctttccctgtagttgtgtccatttcccctccctgg------cttctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttg -tgtccatttcccctccctggctt---ctcctgtagcatctttcc---------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------tagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -tttcccctccctggcgtctcctcctgcagcatctttcc---tagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctc---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------ccatttcccctccctggcttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctg -gtagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggt -gtggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga ->p:HG002_2_chr20:64173308-64176630 -acagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctc -cccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccata -ccccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatcctt -ccctttagttgtgtccatttcccctccctgacttctcctcctgcagcatctttcctagtt -gtgtccatttcccctccctgacttctcctcctgcagcatctttccttgtagttgtgtcca -tttcccctccctggcttctcctcctgcagcatctttcctagttgtgtccatttcccctcc -ctgacttctcctcctgcagcatccttccctgtagttgtgtccatttcccctccctgactt -ctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctgacttctcctcc -tgcagcatctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagca -tctttccctgtagttgtgtccattccccctccctggcttctcctgtagcatctttccctg -tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtc -catttcccctccctggctt----------------------------------------- ----------------ctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatt -tcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc ----tagttgtgtccatttcccctccctggctt---------------------------- -----------------------ctcctgcagcatctttccctgtagttgtgtccatttcc -cctccctggcttctcctgtagcaactttcctagttgtgtccatttcccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttcc-------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------tagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttg -tgtccattccccctccctggctt---ctcctgtagcatctttccctgtagttgtgtccat -ttcccctccctggcttctgcagcatctttccctgtagttgtgtccatttcccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgtagcatctttcc---ta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgtagcatctttcc---tagttgtgtccatttcccctccctggcttctcctgcagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -tttcccctccctggcgtctcctcctgcagcatctttcc---tagttgtgtccatttcccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt -ctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctcctcc -tgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagca -tctttccctgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctc -cctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccc -tgtagttgtgtccattccccctccctggcttctcctcctgcagcatctttccctgtagtt -gtgtccatttcccctccctggcttctgcagcatctttccctgtagttgtgtccatttccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgtagcatctttccctgtagttgtgttcatttcccctc -cctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcat -ctttccctgtagttgtgtccatttcccctccctgg---cttctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------ccatttcccctccctggcttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctg -gtagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggt -gtggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga ->ref_chr20:64173308-64176630 -acagaggtgggctgttggacaggtgcggctgatagagtgggtgtcttttgtgggcttctc -cccagcctgtggcctggcctagtcagtagagatggtcaggggagcaggagggagcccata -ccccagtgcctgtagttgtgtccatttcccctccctgacttctcctcctgcagcatcctt -ccctt--------------------------------------------------tagtt -gtgtccatttcccctccctgacttctcctcctgcagcatccttccctttagttgtgtcca -tttcccctccctgacttctcctcctgcagcatctttcctagttgtgtccatttcccctcc -ctgacttctcctcctgcag----------------------------------------- ------------------------------------------------------------- ------catctttccttgtagttgtgtccatttcccctccctggcttctcctcctgcagca -tctttccttgtagttgtgtccatttcccctccctgacttctc------------------ ------------------------------------------------------------- ------------------------------------------------------------- ----------------ctcctgcagcatccttccctgtagttgtgtccatttcccctccct -ggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcct -gcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctt -tccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttccctg---- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------tagttgtgtccattccccctccctggcttctcct -gtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttcc -ctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttgtgtc -catttcccctccctggcttctcctcctgcagcatctttccctgtagttgtgtccattccc -cctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttc -tcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtag -ttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtccat -ttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattccccctccc -tgacttctc--------------------------------------------ctcctgc -agcatctttccctgtagttgtgtccatttcccctccctggcgtctcctcctgcagcatct -ttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatctttcctagttg -tgtccatttcccctccctggcttctcctcctgcagcatctttcc---------------- --------------------------------ctgtagttgtgtccattccccctccctgg -cttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttctcctgtagc -atctttcctagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcca -tttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctcc -ctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc -ctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcatc -tttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgta -gttgtgtccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtcca -ttccccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccattccccc -tccctggcttctcctgcagcatctttccctgtagttgtgtccatttcccctccctggctt ----ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctc---c -tgtagcatctttcc---tagttgtgtccatttcccctccctggctt---ctcctgcagca -tctttccctgtagttgtgtccatttcccctccctggctt---ctcctgtagcatctttcc -ctgtagttgtgtccattccccctccctgacttctcctcctgcagcatctttccctgtagt -tgtgtccatttcccctccctggcgtctcctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgtagcatctttcc------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ----------tagttgtgtccatttcccctccctggcttctcctcctgcagcatctttccc -tgtagttgtgtccattc------------------------------------------- ----------------------------------------------------------ccc -ctccctggcttctcctgtagcatctttcctagttgtgtccatttcccctccctggcttct -cctgtagcatctttcc-------------------------------------------- ----------tagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgt -agttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtgtcc -atttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccatttcccctc -cctggcttctcctgcagcatctttcc---tagttgtgtccatttcccctccctggcttct -cctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgtagcat -ctttccctgtagttgtgtccattccccctccctggcgtctcctcctgcagcatctttccc -tgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccctgtagttgtg -tccatttcccctccctggcttctcctgtagcatctttccctgtagttgtgtccattcccc -ctccctggcgtctcctcctgcagcatctttccctgtagttgtgtccatttcccctccctg -gcttctcctcctgcagcatctttccctgtagttgtgtccattccccctccctggcttctc -ctcctgcagcatctttccctgtagttgtgtccatttcccctccctggcttctcctgcagc -atctttccctgtagttgtgtccatttcccctccctggcttctcctgcagcatctttccct -gtagttgtgtccatttcccctccctggcttctcctcttctagcatctttcctgctccctg -gtagcctcttgggagccacctatttctggaggtccccactctgggttccttgtcctgggt -gtggggcgaatgtgctggactggggtcacagcattgaaccccacttggagctgagga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c8767647c15df9e79d6194de26f7cdc5.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c8767647c15df9e79d6194de26f7cdc5.msa deleted file mode 100644 index 9635edad..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c8767647c15df9e79d6194de26f7cdc5.msa +++ /dev/null @@ -1,480 +0,0 @@ ->syndip_1_chr20:20354470-20358423 -tccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaaatcaggtac -agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata -agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgagg -gaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacac -tgtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggt -ggtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagag -aaaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgt -gtcagaggaggtggtcacactgaggggaggtggtcacactgtgagaggggaggtggtcag -actctgtcagaggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtg -gtcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagagggg -aggtgatcacactgagggg-----------------------aggtggtcacactgtgag -agggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtca -cactgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggagaa -ggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtg -gtcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtc -acactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggt -cacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtgg -tcacactgaggggaggtactcacactgtgaggggaggtggtcacactgtgaggggaggtg -gtcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggg -ggtcacactgtgagggggaaggtggtcacactgtgagaggggagaaggtcacactaaggg -gaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgaga -ggaggtggtcacactgtgaggggaggtcacactgaggggaggtagtgacactatgagcag -agatggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagca -gagatggtcacactgtgaggggaggtggtcacactgaggggaggtagtcacactgtgagg -ggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgag 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-acactgaggggaggtggtcacagtgtgaggggaggtggtcacac---------------- -------------------------tgaggggaggtggtcatagtgtgaggggaggtggtc -acactggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcaca--ctgaggggaggtggtcatag -tgtgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcacactgt -gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag -gggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcatactgtga -gtgaggaggtagtcacac--tgaggggagggggtcatactgcgagtggaggtagtcacac -tgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcatactg---------------------------------------- -tgaggggaagtggtcacactgaggggaggtggtcatagtgtga--ggggaggtggtcaca -ctgaggggaggtggtcacagtgtgaggggaggtggtcacac--tgaggggaggtggtcac -actgaggggaggtggtcacagtgtgagaggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac 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-actgaggggaggtggtcaca-c-tgaggagaggtggtcat-------------------a -gtgtgaggggaggtggtcacac-------------------------------------- ------------------------------------------------------------- ----tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -actgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacagtg----------------- ----------------------tgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgtgaggggaggtggtcacattgaggagaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgaggagaggtggtcatagtgtgcggggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacagtg -tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg -aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact -gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg -tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcacactgaggggaatggtcatactgtga -ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg -ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc -aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag -tggttttacgctatttaacccagtgtcag ->syndip_2_chr20:20354470-20358423 -tccagtctgggtgacagagagagaccttgtctc--aaaaaaaaaaaaaaaaatcaggtac -agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata -agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgagg -gaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacac -tgtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggt -ggtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagag -aaaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgt -gtcagaggaggtggtcacactgaggggaggtggtcacactgtgagaggggaggtggtcag -actctgtcagaggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtg -gtcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagagggg -aggtgatcacactgaggggaggtggtcacactgtgagagggaaggtggtcacactgtgag -agggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtca -cactgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggagaa -ggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtg -gtcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtc -acactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggt -cacactgaggggaggtagtgacactgtgagcagaga------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----tggtcacactgtgaggggaggtggtcacactgaggggaggtactcacactgtgagg -ggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgag -cagagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacact 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-cagtg-------------------tgaggggaggtggtcatagtgtgaggggaggtggtc -acactggggaggtggtcacactgtgaggggaggtggtcacactgtgaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac -t----ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacact---------------------ggggaggtggtcacactgt -gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag -gggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac----- --tggggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacac ---tgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacac -tgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac -actgagaggaggtggtcaca--ctgaggggaagtggtcacactgaggggaggtggtcata -ctgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca 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-gaggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtga -ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg -ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc -aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag -tggttttacgctatttaacccagtgtcag ->p:HG002_1_chr20:20354470-20358423 -tccagtctgggtgacagagagagaccttgtctc--aaaaaaaaaaaaaaaaatcaggtac -agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata -agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgagg -gaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacac -tgtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggt -ggtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagag -aaaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgt -gtcagaggaggtggtcacactgaggggaggtggtcacactgtgagaggggaggtggtcag -actctgtcagaggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtg -gtcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagagggg -aggtgatcacactgaggggaggtggtcacactgtgagagggaaggtggtcacactgtgag -agggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtca -cactgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggagaa -ggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtg -gtcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtc -acactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggt -cacactgaggggaggtagtgacactgtgagcagaga------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----tggtcacactgtgaggggaggtggtcacactgaggggaggtactcacactgtgagg -ggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgag -cagagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacact -gtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatcac 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-ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg -ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc -aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag -tggttttacgctatttaacccagtgtcag ->p:HG002_2_chr20:20354470-20358423 -tccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaaatcaggtac -agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata -agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgagg -gaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacac -tgtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggt -ggtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagag -aaaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgt -gtcagaggaggtggtcacactgaggggaggtggtcacactgtgagaggggaggtggtcag -actctgtcagaggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtg -gtcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagagggg -aggtgatcacactgagggg-----------------------aggtggtcacactgtgag -agggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtca -cactgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggagaa -ggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtg -gtcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtc -acactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggt -cacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtgg -tcacactgaggggaggtactcacactgtgaggggaggtggtcacactgtgaggggaggtg -gtcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggg -ggtcacactgtgagggggaaggtggtcacactgtgagaggggagaaggtcacactaaggg -gaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgaga -ggaggtggtcacactgtgaggggaggtcacactgaggggaggtagtgacactatgagcag -agatggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagca -gagatggtcacactgtgaggggaggtggtcacactgaggggaggtagtcacactgtgagg -ggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgag -cagagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacact -gtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatcac -actaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcacac 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-ctgaggggaagtggtcacactgaggggaggtggtcaca--ctgaggggaggtggtcatag -tgtgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtcacactgt -gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag -gggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcatactgtga -gtgaggaggtagtcacac--tgaggggagggggtcatactgcgagtggaggtagtcacac -tgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggtcacact -gaggggaggtggtcatactg---------------------------------------- -tgaggggaagtggtcacactgaggggaggtggtcatagtgtga--ggggaggtggtcaca -ctgaggggaggtggtcacagtgtgaggggaggtggtcacac--tgaggggaggtggtcac -actgaggggaggtggtcacagtgtgagaggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcacag -tgtgaggggagatggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcaca -ctgaggggaggtggtcaca-------------------gtgtgaggggaggtggtcacac -tgaggggaggtggtcacactgagaggaggtggtcacactgaggggaggtggtcatactgt -gagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtg--------- ----------------------------------gtcacactgaggggagggggtcatact -gcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcacac -tgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtcacact -gaggggaggtggtcatagtgtgaggggag------------------------------- ------------------------------------------------------------- -----------gtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg -tga--ggggaggtggtcacactgaggggaggtggtcacagtgtacggggaggtggtcata -c--tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcac -actgaggggaggtggtcaca-c-tgaggagaggtggtcat-------------------a -gtgtgaggggaggtggtcacac-------------------------------------- ------------------------------------------------------------- ----tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -actgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacagtg----------------- ----------------------tgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgtgaggggaggtggtcacattgaggagaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacactgaggagaggtggtcatagtgtgcggggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcacagtg -tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg -aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact -gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg -tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact -gaggggaggtggtcacactgaggggaggtggtcacactgaggggaatggtcatactgtga -ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg -ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc -aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag -tggttttacgctatttaacccagtgtcag ->ref_chr20:20354470-20358423 -tccagtctgggtgacagagagagaccttgtctca-aaaaaaaaaaaaaaaaatcaggtac -agaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcata -agggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatagtcacactgagg -gaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcacac -tgtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggaggt -ggtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgagag -aaaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactgt -gtcagaggaggtggtcacactgagg----------------------------------- ------------ggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagtg -gtcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagagggg -aggtgatcacactgagggg-----------------------aggtggtcacactgtgag -agggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtca -cactgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggagaa -ggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtg -gtcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggtc -acactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggt -cacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtgg -tcacactgaggggagg-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----tggtcacactgtgaggggaggtggtcacactgaggggaggtggtcacactgtgagg -ggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgag -cagagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacact -gtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatcac -actaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcacac -tgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcaca -ctgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtcac -actgaggggaggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtca -cactgaggggaggtagtgacactgtgagcagagatggtcacactgtaaggggaggtgatc -acactgtgaggggac---gtcacactgtgaggggaggtggtcacactgtgagaggggagg -tgaccacacaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatgg -tcacactgtgaggggaggtggtcacac--tgaggggaggtagtcacactgagaggaggtg -gtcacactgaggggaagtggtcacactgagggggggtggtcacactgaggggaggtggtc -atactgtgagtgaggagctagtcacactgaggggaggggtcatactgcgagtggaggtag -tcacactgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtggt -cacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtc -atagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtca -cagtgtgaggggagg----------------------------------------tggtc -acactgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtca -cagtgtgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtc -acactggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac -t----ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtg -tgaggggaggtggtcacact---------------------ggggaggtggtcacactgt -gaggggaggtggtcacactgagaggaggtggtcacactgaggggaagtggtcacactgag -gggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac----- --tggggaggtggtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacac ---tgagaggaggtggtcacactgaggggaagtggtcacactgagaggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacac -tgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac -actgagaggaggtggtcaca--ctgaggggaagtggtcacactgaggggaggtggtcata -ctgtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------gtgtgcggggaggtggtcatac -tgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatactgt -gagt-------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------gaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcaca -ctgtgaagggtggtagtcaca--ctgagaggaggtggtcacactgaggggaagtggtcac -actgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcata -gtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacagtgtgcggggaggtggtcat-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------actgaggggaggtggtcacagtgtgaggggaggtggtcacagtg -tgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacact -gaggggaggtggtcacactgagggaaggtggtcacactgaggggaggtggtcatagtgtg -aggggaggtggtcatagtgtgaggggaggtggtcacagtgtgaggggaggtggtcacact -gaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacactg -tgaggggaggtgggcacactgtgaggggtggtagtcacactgagaggaggtggtcacact -gaggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtga -ggggaggtggtcacactgaggggaagtggtcacactgaggggaatggtcatactgtgagg -ggaggtggtcacactgtgaaagaagatgatcacagtatgagaggtcatccttcaagaggc -aagtgcccaaaaatctgtttataatctagagcaatatttgcctgaaataaactttaaaag -tggttttacgctatttaacccagtgtcag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_c9e1dbc9a9539b28dd314cc389412191.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_c9e1dbc9a9539b28dd314cc389412191.msa deleted file mode 100644 index 3ef1edb9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_c9e1dbc9a9539b28dd314cc389412191.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:35580576-35580866 -ggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactc -tgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatatatat -atat-atatatatataatatatatatatataaaatatatatatataaaatatatatatat -ataaaatatatatatataaaatatatatatatatataaaatatatatatataaaatatat -atatataaaatatatatatatataaaatatatatatatataaaatatatatatataaaat -atatatatatataaaatatatatatataaaatatatatatataaaatatatatatatata -aaatatatatatataaaatatatatatataaaatatatatatatataatatatatatata -aaatatatatatat--aaaatatatataaaatatatatatataaaatatatatataatat -atatatataaaatatatatatataatatatatatataaaatatatatatataaaatatat -atatatataaaatatatatatatataaaatatatatatggaattccat ->syndip_2_chr20:35580576-35580866 -ggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactc -tgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatatat-- --------atatatatatataaaatatatataaaatatatatatata-------------- --------atatatatataaaatatatatatat------aatatatatatataaaatatat -atatataaaatatatatatatataaaatatatatatatataaaatatatatatggaa--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------ttccat ->p:HG002_1_chr20:35580576-35580866 -ggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactc -tgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatat---- -----------------------atatatataaaatatatatatataaaatatatatat-- -----aatatatatatataaaatatatatatat------aatatatatatataaaatatat -atatataaaatatatatatatataaaatatatatatatataaaatatatatatggaa--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------ttccat ->p:HG002_2_chr20:35580576-35580866 -ggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactc -tgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatatatat -atataaaatatatatatataatatatatataaaatatatatatataaaatatatatatat -ataaaatatatatatataaaatatatatatatatataaaatatatatatataaaatatat -atatataaaatatatatatatataaaatatatatatatataaaatatatatatataaaat -atatatatatataaaatatatatatataaaatatatatatataaaatatatatatatata -aaatatatatatataaaatatatatatataaaatatatatatatataatatatatatata -aaatatatatatataaaaaatatatataaaatatatatatataaaatatatatataatat -atatatataaaatatatatatataatatatatatataaaatatatatatataaaatatat -atatatataaaatatatatatatataaaatatatatatggaattccat ->ref_chr20:35580576-35580866 -ggcacaggttgcagtgagccgagatcgcgccactgcagcctaggcagcagagtgagactc -tgtcttaaaatatatattatggtttattttattttatggttaaaggccatatatatatat -atataaaatatatatatataaaatatatataaaatatatatatataaaatatatatat-- -----aatatatatatataaaatatatatatat------aatatatatatataaaatatat -atatataaaatatatatatatataaaatatatatatatataaaatatatatatggaa--- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------ttccat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ccc0fcb16c1bbefd1880192780069e96.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ccc0fcb16c1bbefd1880192780069e96.msa deleted file mode 100644 index 254870d1..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ccc0fcb16c1bbefd1880192780069e96.msa +++ /dev/null @@ -1,180 +0,0 @@ ->syndip_1_chr20:20337175-20337734 -aagcagccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggat -ggatgcatggatggatggatggatggacagaatgggtgggtggatggatggatggatgga -tggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggataga -tgggtggatggataaatggatggatggatggatggatagatgggtgggtagatggatgga -tggatggatggatggatggatggatggatggatggatagatgggtgggtgggtggatgga -tggatggatggatggatggatggatggatagatgggtgggtggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatgggtggatggataaatggatggatggatggatggatagatgggtggg -tggatggatggatggatggatggatggatggatggatagatagatggatagatgggtggg -tggatggatggatggatggatggatggatggatggatggatagatgggtggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatggatggatggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatgggtgggtgggtggatggatggatgga -tggatagaataaaaaagaaagctaggacatggttctagtgttcttagcagacgtcccacc -at ->syndip_2_chr20:20337175-20337734 -aagcagccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggat -ggatgcatggatggatggatggatggacagaatgggtgggtggatggatggatggatgga -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtggatgga -taaatggatggatggatggatggatagatgggtgggtaga----tggatggatggatgga -tggatggatggatggatggatggatggatagatgggtgggtgggtggatggatggatgga -tggatggatggatggatggatggatggatagatgggtgggtggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatgggtggatggataaatggatggatggatggatggatagatgggtggg -tggatggatggatggatggatggatggatggatggataga----------------tggg -tgggtggatggatggatggatggatggatggatggatggatagatgggtggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatgga -tagatgggtggg----tggatggatggatggatggatggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggata--------------------gatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatg----------------gatggatagatgggtggg -tgggtggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtgggtggatggatggatggatggataga---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------ataaaaaagaaagctaggacatggttctagtgttcttagcagacgtcccacc -at ->p:HG002_1_chr20:20337175-20337734 -aagcagccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggat -ggatgcatggatggatggatggatggacagaatgggtgggtggatggatggatggataga -tggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtggg -tggatggatggatggatggatggatggatggatggatgga----tggatagatgggtggg -tggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggatagatgggtggatggataaatggatggatggatggatgga -tagatgggtgggtggatggatggatggatggatggatggatggatggatagatggatgga -tagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatgggtggatggataaatggatggatggatggatggatagatgggtggg -tggatggatggatggatggatggatggatagatggataga----------------tggg -tgggtggatggatggatggatggatggatggatggatggatagatgggtggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatgga -tagatgggtggg----tggatggatggatggatggatggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggata--------------------gatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatg----------------gatggatagatgggtggg -tgggtggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatgggtggatggatggatggatagatgggtgggtgggtgga -tggatggatggatggatagatgggtgggtgggtggatggatggatggatggataga---- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------ataaaaaagaaagctaggacatggttctagtgttcttagcagacgtcccacc -at ->p:HG002_2_chr20:20337175-20337734 -aagcagccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggat -ggatgcatggatggatggatggatggacagaatgggtgggtggatggatggatggatgga -tggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggataga -tgggtggatggataaatggatggatggatggatggatagatgggtgggtggatggatgga -tggatggatggatggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatggatggatggatggatggatggatagatgggtgggtggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatgggtggatggataaatggatggatggatggatggatagatgtgtggg -tggatggatggatggatggatggatggatggatggatggatagatggatagatgggtggg -tggatggatggatggatggatggatggatggatggatggatagatgggtggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatggatggatggatggatggatggatagatgga -tagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatagatggatggatggatggatggatgga -tggatggatggatggatggatagatgggtgggtgggtggatggatggatggatggatgga -tggatggatggatggatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggg -tggatggataaatggatggatggatggatggatagatgggtgggtggatggatggatgga -tggatggatggatggatggatagatagatgggtgggtggatggatggatggatagatggg -tgggtgggtggatggatggatggatggatagatgggtgggtgggtggatggatggatgga -tggatagaataaaaaagaaagctaggacatggttctagtgttcttagcagacgtcccacc -at ->ref_chr20:20337175-20337734 -aagcagccactggaaataaggaaacagggtttaggaaggcctcactagacctgttaggat -ggatgcatggatggatggatggatggacagaatgggtgggtggatggatggatggataga -tggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtggg -tggatggatggatggatggatggatggatggatggatgga----tggatagatgggtggg -tggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggatagatgggtggatggataaatggatggatggatggatgga -tagatgggtgggtggatggatggatggatggatggatggatggatggatagat------- ----------------gtgggtggatggatggatggatagatgggtgggtgggtggatgga -tggatggatggatagatgggtgggtgggtggatggatggatggatggataga-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------ataaaaaagaaagctaggacatggttctagtgttcttagcagacgtcccacc -at diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cded8ffb9ddab864fcc8e3347b21349f.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cded8ffb9ddab864fcc8e3347b21349f.msa deleted file mode 100644 index 3a5f318b..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cded8ffb9ddab864fcc8e3347b21349f.msa +++ /dev/null @@ -1,195 +0,0 @@ ->syndip_1_chr20:63027956-63029140 -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagagggccggt -ggggagaggaccggtggggagggggccggtggagagggggccggtggggagggggccggt -ggggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtg -gggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtggg -gagggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtggg -gagggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggg -agggggccggcggggagggaccggtggggaggggccggtggggtggggccggtggagagg -gggccggtggggagggggccggcggggagtggtttggtggggaggaggctggtgaagtag -cgtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctg -cagcttcatcaggttctcaattagcggagggcgctggcggtggaggagggcattagccgt -gcctgctctcgggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagc -ctctttcctgacagcaggttttccatttttcttctccttcctcctctcctggcaacaaag -tcctttgctgggctggggggtctccactctgatccacttccctccttcctgcctccctcc -cacgccctggaaaccccggcccatgactctttccctgagggggccgcccgcagcctctcc -cccatgggggctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgg -gactcaggaagatggtggcccagtggggctctctccttgggtgtgtgggagcggagtccc -ctcgctcttctgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctc -tgggggagggagtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcct -ttttaagcagctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgc -tgggaggcgcaggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgtt -atttcccatgatgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcctctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtg -tgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctg -tgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -tctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgtctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctc -cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccggg -cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg -ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccc -cgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcc -cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggt -cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag -gtcccccgggcctccgc ->syndip_2_chr20:63027956-63029140 -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggt -ggggag-gggccggtggagagggggccggtggggagggggccggcggggag--------- ---------------------tggtttggtggggagggggccggtggggagggggcctgcg -gggaggggccggtggggag-----------------------------ggggccggtggg -gagggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtggg -gag-----------------------------ggggccggtggggagggggccggcgggg -agggggccggcggggaggggccggtggggagtggt-------------ctggtggggagg -gggcc------------------------------ggtggggaggaggctggtgaagtag -cgtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctg -cagcttcatcaggttctcaattagcggagggcgctggcggtggaggagggcattagccgt -gcctgctctcgggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagc -ctctttcctgacagcaggttttccatttttcttctccttcctcctctcctggcaacaaag -tcctttgctgggctggggggtctccactctgatccacttccctccttcctgcctccctcc -cacgccctggaaaccccggcccatgactctttccctgagggggccgcccgcagcctctcc -cccatgggggctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgg -gactcaggaagatggtggcccagtggggctctctccttgggtgtgtgggagcggagtccc -ctcgctcttctgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctc -tgggggagggagtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcct -ttttaagcagctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgc -tgggaggcgcaggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgtt -atttcccatgatgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------ ->p:HG002_1_chr20:63027956-63029140 -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggt -ggggag-gggccggtggagagggggccggtggggagggggccggcggggag--------- ---------------------tggtttggtggggagggggccggtggggagggggcctgcg -gggaggggccggtggggag-----------------------------ggggccggtggg -gagggggccggcggggagggggccggcggggagggggccggcggggagtggtctggtggg -gag-----------------------------ggggccggtggggagggggccggcgggg -agggggccggcggggaggggccggtggggagtggt-------------ctggtggggagg -gggcc------------------------------ggtggggaggaggctggtgaagtag -cgtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctg -cagcttcatcaggttctcaattagcggagggcgctggcggtggaggagggcattagccgt -gcctgctctcgggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagc -ctctttcctgacagcaggttttccatttttcttctccttcctcctctcctggcaacaaag -tcctttgctgggctggggggtctccactctgatccacttccctccttcctgcctccctcc -cacgccctggaaaccccggcccatgactctttccctgagggggccgcccgcagcctctcc -cccatgggggctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgg -gactcaggaagatggtggcccagtggggctctctccttgggtgtgtgggagcggagtccc -ctcgctcttctgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctc -tgggggagggagtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcct -ttttaagcagctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgc -tgggaggcgcaggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgtt -atttcccatgatgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtg -caggtcccccgggcctccgc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------ ->p:HG002_2_chr20:63027956-63029140 -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggt -ggggag-gggccggtggagagggggccggtggggagggggccggtggggagggggccggt -ggggagaggaccggtggggaggggccggtggggagggggccggtggggagaggaccggtg -gggaggggccggtggggagggggccggtggggagaggaccggtggggaggggccggtggg -gagggggccggcggggagggggccggcggggagggtgccggtggggagtggtctggtggg -gagggggccggtggggagggggcccgcggggaggggccggtggggagggggcctgcgggg -agggggccggcggggaggggccggtggggaggggccggtggggtggggccggtggggagg -gggccggtgggg-gggggcctgcggggagtggtttggtggggaggaggctggtgaagtag -cgtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctg -cagcttcatcaggttctcaattagcggagggcgctggcggtggaggagggcattagccgt -gcctgctctcgggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagc -ctctttcctgacagcaggttttccatttttcttctccttcctcctctcctggcaacaaag -tcctttgctgggctggggggtctccactctgatccacttccctccttcctgcctccctcc -cacgccctggaaaccccggcccatgactctttccctgagggggccgcccgcagcctctcc -cccatgggggctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgg -gactcaggaagatggtggcccagtggggctctctccttgggtgtgtgggagcggagtccc -ctcgctcttctgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctc -tgggggagggagtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcct -ttttaagcagctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgc -tgggaggcgcaggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgtt -atttcccatgatgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcctctccgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtg -tgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctc -cgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcc -tccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -tctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccg -cgtctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctc -cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccggg -cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg -ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccc -cgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcc -cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggt -cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag -gtcccccgggcctccgc ->ref_chr20:63027956-63029140 -gctcaggcccctcctctccaaggtcccagctgtccttgccctgttccctgtgaagagtga -agaaccaacgcgggcggggagtggaccggtggggagagggccggtggggagaggaccggt -ggggag-gggccggtggagagggggccggtggggagggggccggcggggag--------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------tggtttggtggggaggaggctggtgaagtag -cgtcaggtgcgggcctggcgtcggcgagtcaagtcgagctgatccagggccttctttctg -cagcttcatcaggttctcaattagcggagggcgctggcggtggaggagggcattagccgt -gcctgctctcgggctctgcctgccagagtgccctcatgtggcatgagattaaggctcagc -ctctttcctgacagcaggttttccatttttcttctccttcctcctctcctggcaacaaag -tcctttgctgggctggggggtctccactctgatccacttccctccttcctgcctccctcc -cacgccctggaaaccccggcccatgactctttccctgagggggccgcccgcagcctctcc -cccatgggggctttgctctgggcaccccctttcccccggggcgggtggggcagcggccgg -gactcaggaagatggtggcccagtggggctctctccttgggtgtgtgggagcggagtccc -ctcgctcttctgggatagaacgctccgttgagctccccaaactgctcccgtgccgagctc -tgggggagggagtctgttcagagacggtgcagtcctaccttttagaaggtacgcctgcct -ttttaagcagctcagctctcaacaatgcacaagtggcttgagtagaagagctgctcctgc -tgggaggcgcaggaggctgagcgaggcccaccctgcaggggcgaggccacggtttgtgtt -atttcccatgatgactccaaacgcacccgagtcccccgggcctccgcgcctccgtgtgca -ggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtg -caggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtg -tgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccg -tgtgcaggtcccccgggcctccgc------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------ diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ce49df5cbcfc9e891ed27ea7b2757f5c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ce49df5cbcfc9e891ed27ea7b2757f5c.msa deleted file mode 100644 index 07c6d91e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ce49df5cbcfc9e891ed27ea7b2757f5c.msa +++ /dev/null @@ -1,260 +0,0 @@ ->syndip_1_chr20:63491488-63493165 -ggtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagcc -cactggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggttt -ctcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggat -ggatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggt -ggggagatggatgagtagggagatggatggatggattggtggatggatggatggatggat -ggatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggat -gaatggatggatggggaggtggatggatagatggatggatggatggatggatggatggat -ggatggatggggggatagatggatggatggatggatggatggacggacg----gatgggg -aggtggatggatggatggatggatggatggatggatggatgaggagatgaatggatggat -gagatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagag -aggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggat -ggggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggg -agatggatggatggatggatggggagggatggatggatggatggatggatgggtggatgg -atagaaggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatgg -atagatggata----gatggatggatggatggatggatggagagaaggatggatgggtgg -ggaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgg -atggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtgg -ggaggtgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatgg -atggatggatgcatggatggatgga----------------------------------- ------------------------------------------------------------- ---------------------tggagaggtgggtggacggatggatggattgggaggtggg -tagatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatgga -tggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatgga -cagaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatgga -tggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatgga -cgggtggggagatggatggatggatggatggatggatggatggatggacagaaggatgta -tgggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatgga -aggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatgga -tgggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatggg -tgggacaatagatggatggatagagagaaggatggatgggtggggagatggatggatgga -tggatggatggatggatggatggatggatagagagaaggatggatggttgagaca----a -tggatggatggatggatggagagatggatggatggacggatggacagaaggatggatggg -tggggaggtggatggatggattgaaggatggatgggtgggga----catggatggatgga -tggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggata-- -------gatggatggatggggaaatggatggatggaaggatggatggatagggaggtggg -tggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtgga -tgaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggataga -gagaaggatggatgggtggggagatggatggatggatggatggatggatggatagagaga -aggatggatggttgagacaatggatggatggatggatggatggagagatggatggatgga -tggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatgga -tggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatgga -tggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatgga -tggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatgga -tggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatgga -gagatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatgga -tggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatgga -tagatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggat -gggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgt -gtggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggt -ctagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaa -tcttgtacacgtcctgcagcggc ->syndip_2_chr20:63491488-63493165 -ggtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagcc -cactggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggttt -ctcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggat -ggatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggt -ggggagatggatgagtagggagatggatggatggattggtggatggatggatggatggat -ggatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggat -gaatggatggatggggaggtggatggatagatggatggatggatggatggatggatggat -ggatggatggggggatagatggatggatggatggatggacggacggatggggaggtggat -ggatggatggatggatggatggatggatggatggatggatgaggagatgaatggatggat -gagatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagag -aggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggat -ggggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggg -agatggatggatggatggatgcggagggatggatggatggatggatggatgggtggatgg -atagaaggatggatgggtggggaggtgggtgggtgggtgcgtggatggatggagagatgg -atagatggatagatggatggatggatggatggatggatggagagaaggatggatgggtgg -ggaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgg -atggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtgg -ggaggtgggtgggtggatggatggatgagtggggaggtgggtgggtggatggatggatgg -atggatgcatggatggatggatggagaggtgggtggatgggtggatggacagaaggatgg -atgggtggggaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatgg -atggatgaaggatggatgggtggggaggtgggtggacggatggatggattgggaggtggg -tagatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatgga -tggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatgga -cagaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatgga -tggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatgga -cgggtgggga----gatggatggatggatggatggatggatggatggacagaaggatgta -tgggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatgga -aggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatgga -tgggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatggg -tgggacaatagatggatggatagagagaaggatggatgggtgggga--------gatgga -tggatggatggatggatggatggatggatagagagaaggatggatggttgagacaatgga -tggatggatggatggatggagagatggatggatggatggatggacagaaggatggatggg -tggggaggtggatggatggattgaaggatggacgggtggggagatggatggatggatgga -tggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggataga -tggatggatggatggatggggaaatggatggatggaaggatggatggatagggaggtggg -tggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtgga -tgaatggatggatggatagatagaaggatggatgggtgggacaaca----gatggataga -gagaaggatggatgggtgggga----gatggatggatggatggatggatggatagagaga -aggatggatggttgagacaatggatggatggatggatggatggagagatggatggatgga -tggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatgga -tggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatgga -tggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatgga -tggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatgga -tggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatgga -gagatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatgga -tggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatgga -tagatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggat -gggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgt -gtggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggt -ctagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaa -tcttgtacacgtcctgcagcggc ->p:HG002_1_chr20:63491488-63493165 -ggtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagcc -cactggctgggggtctcctatcagtgcccttctctggggtctcagatttgtttatggttt -ctcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggat -ggatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggt -ggggagatggatgagtagggagatggatggatggattggtggatggatggatggatggat -ggatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggat -gaatggatggatggggaggtggatggatagatggatggatggatggatggatggatggat -ggatggatggggggatagatggatggatggatggatggacggacggatggggaggtggat -ggatggatggatggatggatggatggatggatggatggatgaggagatgaatggatggat -gagatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagag -aggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggat -ggggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggg -agatggatggatggatggatgcggagggatggatggatggatggatggatgggtggatgg -atagaaggatggatgggtggggaggtgggtgggtgggtgcgtggatggatggagagatgg -atagatggatagatggatggatggatggatggatggatggagagaaggatggatgggtgg -ggaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgg -atggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtgg -ggaggtgggtgggtggatggatggatgagtggggaggtgggtgggtggatggatggatgg -atggatgcatggatggatggatggagaggtgggtggatgggtggatggacagaaggatgg -atgggtggggaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatgg -atggatgaaggatggatgggtggggaggtgggtggacggatggatggattgggaggtggg -tagatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatgga -tggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatgga -cagaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatgga -tggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatgga -cgggtgggga----gatggatggatggatggatggatggatggatggacagaaggatgta -tgggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatgga -aggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatgga -tgggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatggg -tgggacaatagatggatggatagagagaaggatggatgggtgggga--------gatgga -tggatggatggatggatggatggatggatagagagaaggatggatggttgagacaatgga -tggatggatggatggatggagagatggatggatggatggatggacagaaggatggatggg -tggggaggtggatggatggattgaaggatggacgggtggggagatggatggatggatgga -tggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggataga -tggatggatggatggatggggaaatggatggatggaaggatggatggatagggaggtggg -tggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtgga -tgaatggatggatggatagatagaaggatggatgggtgggacaaca----gatggataga -gagaaggatggatgggtgggga----gatggatggatggatggatggatggatagagaga -aggatggatggttgagacaatggatggatggatggatggatggagagatggatggatgga -tggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatgga -tggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatgga -tggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatgga -tggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatgga -tggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatgga -gagatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatgga -tggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatgga -tagatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggat -gggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgt -gtggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggt -ctagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaa -tcttgtacacgtcctgcagcggc ->p:HG002_2_chr20:63491488-63493165 -ggtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagcc -cactggctgggggtctcctatcagtgcccttctctggggtctcagatttgtttatggttt -ctcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggat -ggatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggt -ggggagatggatgagtagggagatggatggatggattggtggatggatggatggatggat -ggatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggat -gaatggatggatggggaggtggatggatagatggatggatggatggatggatggatggat -ggatggatggggggatagatggatggatggatggatggatggacggacg----gatgggg -aggtggatggatggatggatggatggatggatggatggatgaggagatgaatggatggat -gagatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagag -aggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggat -ggggaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtaggg -agatggatggatggatggatggggagggatggatggatggatggatggatgggtggatgg -atagaaggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatgg -atagatggata----gatggatggatggatggatggatggagagaaggatggatgggtgg -ggaggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtgg -atggatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtgg -ggaggtgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatgg -atggatggatgcatggatggatgga----------------------------------- ------------------------------------------------------------- ---------------------tggagaggtgggtggacggatggatggattgggaggtggg -tagatgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatgga -tggatggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatgga -cagaaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatgga -tggatagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatgga -cgggtggggagatggatggatggatggatggatggatggatggatggacagaaggatgta -tgggtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatgga -aggatggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatgga -tgggtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatggg -tgggacaatagatggatggatagagagaaggatggatgggtggggagatggatggatgga -tggatggatggatggatggatggatggatagagagaaggatggatggttgagaca----a -tggatggatggatggatggagagatggatggatggacggatggacagaaggatggatggg -tggggaggtggatggatggattgaaggatggatgggtgggga----catggatggatgga -tggatggatggatggatggatggacagaaggatgtatgggtggggaggtgggtggata-- -------gatggatggatggggaaatggatggatggaaggatggatggatagggaggtggg -tggatggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtgga -tgaatggatggatggatagatagaaggatggatgggtgggacaatagatggatggataga -gagaaggatggatgggtggggagatggatggatggatggatggatggatggatagagaga -aggatggatggttgagacaatggatggatggatggatggatggagagatggatggatgga -tggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatgga -tggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatgga -tggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatgga -tggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatgga -tggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatgga -gagatggagggatggttcgatagagagaaggatggatggatgggacaatggatggatgga -tggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatgga -tagatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggat -gggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgt -gtggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggt -ctagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaa -tcttgtacacgtcctgcagcggc ->ref_chr20:63491488-63493165 -ggtgagcatgatgcccccacagtgcacacagagatgcctgcaacatctttggctgcagcc -cactggctgggggtctcctatcagtgcccttctctagggtctcagatttgtttatggttt -ctcttcttggtgggatggatggatggatggacggatggatggggaggtgggtggatggat -ggatggatgtatgaatggggtggtagatggatggggaggtggatggacagaaggatgggt -ggggagatggatgagtagggagatggatggatggattggtggatggatggatggatggat -ggatgaggaggtagatgagtggatggacagaaggatggatgggtaggaaggtgggtggat -gaatggatggatggggaggtggatggata----gatggatggatggatggatggatggat -ggatggatggggggatagatggatggatggatggatggacggacggatggggaggtggat -ggatggatggatggatggatggatggatggatggatggatgaggagatgaacggatggat -gagatggatggatggatgatggagggaaggatggctgggtggggagatggatggatagag -aggtggatgggtggatggggagatggatggatggatggatggatggggaagtggatggat -ggggaggtggatggat-------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------ggatgta -tgggtgggtaggtgggtggatagatggatg------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------gatggatggatggataaatggatggatggaaggatggatggataggtaggtggg -tggatggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtgga -tgaatggatggatggatagatagaaggatggatgggtgggtcaatagatggatggataga -gagaaggatggatgggtgggta----gatggatggatggatggatggatggatagagaga -aggatggatggttgagacaatggatggatggatggatggatggagagatggatggatgga -tggatggacagaaggatggatgggtggggaggtggatggatggatggaaggatggatgga -tggatagagagaaggatggatgggtgggacaatggatggatggatgcatggatggatgga -tggagggatagagagaaggatggatgggtgggacaatcaatggatggatggatggatgga -tggatagagagaaggatggatgggtggggagatggatggatggatggagaggtggatgga -tggatggatggatggattgatggacagaaggatggatgggtggggaggtggatagatgga -gagatggagggatggttcgatagagagaa----ggatggatgggacaatggatggatgga -tggatggagtgaaggatggatgggtggggagatggatggatcgatggatggatggatgga -tagatagatggatggagaggtggatagatggatgggtggatggatggacagaggatggat -gggtggggaggtgggtggatggatggatggatgtgggatggactgtcccacagaaagtgt -gtggtaaggggagagattggagacagcccagtcttgagatgccttgtaggggcccctggt -ctagggcaggcagagctggccaggcaggagctccagcacagcgcccttgctcaccgccaa -tcttgtacacgtcctgcagcggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_cf4622814e984d95c0e0d70534f49c46.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_cf4622814e984d95c0e0d70534f49c46.msa deleted file mode 100644 index d9c210f4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_cf4622814e984d95c0e0d70534f49c46.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:2240850-2241400 -ctctctgagcctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagc -ggcggctcatcagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttc -tttctttttcctttctttctttctttttctttctttctctctctctccttccttccttct -ttccttccctccctcccttccttttttcttctttctttcattttctttctttctctcttt -cttctttctcttcctttc------------------------------------------ --------------ttctttcttttcctcctt-------cctcccttcttt---------- -----ccttcccttccttcttccctccctccctctttgtttctttctttctctccctc--- ------------------------------------------------------------- ---------------------------------cttccctccctccctttctttctcctt- -----------ttcttccttccctccctgcctgtctccctctttctttctcttttttcttt -tccttccttccgtctttttcctcccttctttcctccctcctccctccctccctcctccct -ctttttctttctttctttc ->syndip_2_chr20:2240850-2241400 -ctctctgagcctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagc -ggcggctcatcagctcacttggaaaatgtagtcatcttctcaaagttttctt-------- ------------tttctttctttctttttctttctttctctctctctccttccttccttct -ttccttccctccctcccttccttttttcttcttcctttcattttctttctttctctcttt -cttctttctcttcctttc------------------------------------------ --------------ttctttcttttcctcctt-------cctcccttcttt---------- -----ccttcccttccttcttccctccctccctctttgtttctttctttctctccctcctt -ccctccctccctttcttccttctttccttatccctcccttctttccttccttccctttgt -ttctctttctttctttctttctctctctcttccttccttccctccctccctccctccttc -ctcccttctttccttccctccctgcctctctgtctccctctttctttctcttttttcttt -tccttccttccgtctttttcctcccttctttcctccctcctccctccctccctcctccct -ctttttctttctttctttc ->p:HG002_1_chr20:2240850-2241400 -ctctctgagcctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagc -ggcggctcatcagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttc -tttctttttcctttctttctttctttttctttctttctctctctctccttccttccttct -ttccttccctccctcccttccttttttcttctttctttcattttctttctttctctcttt -cttctttctcttcctttctttccttccgtccctcccttccttccttttttcttcttcctt -tcattttctttctttctctctttcttctttcctccctttcttccttctttccttatccct -cccttcttcctttcttctttcttttcctccttcctcccttctttccttcccttcctt--- ------------------------------------------------------------- ---------------------------------cttccctccctccctctttgtttctttc -tttctctccctccttccctccctccctttctgtctccctctttctttctcttttttcttt -tccttccttccgtctttttcctcccttctttcctccctcctccctccctccctcctccct -ctttttctttctttctttc ->p:HG002_2_chr20:2240850-2241400 -ctctctgagcctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagc -ggcggctcatcagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttc -tttctttttcctttctttctttctttttctttctttctctctctctccttccttccttct -ttccttccctccctcccttccttttttcttctttctttcattttctttctttctctcttt -cttctttctcttcctttc------------------------------------------ --------------ttctctctttcttctttc----------------------------- -----tcttcctttcttctttcttttcctccttcctcccttctttccttcccttcctt--- ------------------------------------------------------------- ---------------------------------cttccctccctccctctttgtttctttc -tttctctccctccttccctccctccctttctgtctccctctttctttctcttttttcttt -tccttccttccgtctttttcctcccttctttcctccctcctccctccctccctcctccct -ctttttctttctttctttc ->ref_chr20:2240850-2241400 -ctctctgagcctcagtgttgttatctacaaatgggagaatcaaggcaccctcctacaagc -ggcggctcatcagctcacttggaaaatgtagtcatcttctcaaagttttctttttctttc -tttctttttcctttctttctttctttttctttctttctctctctctccttccttccttct -ttccttccctccctcccttccttttttcttctttctttcattttctttctttctctcttt -cttctttctcttcctttctttccttccgtccctcccttccttccttttttcttcttcctt -tcattttctttctttctctctttcttctttc----------------------------- -----tcttcctttcttctttcttttcctccttcctcccttctttccttcccttcctt--- ------------------------------------------------------------- ---------------------------------cttccctccctccctctttgtttctttc -tttctctccctccttccctccctccctttctgtctccctctttctttctcttttttcttt -tccttccttccgtctttttcctcccttctttcctccctcctccctccctccctcctccct -ctttttctttctttctttc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d020210f5e2aeee2a5e670a8c6360e84.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d020210f5e2aeee2a5e670a8c6360e84.msa deleted file mode 100644 index b46f7b63..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d020210f5e2aeee2a5e670a8c6360e84.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:63641678-63642236 -atctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcg -ctgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcc -tcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccc -agtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccga -gctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -ccgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccg -ctccgagctccgccccgg------------------------------------------ ------------------------------------------------------------- --------------------------------ccccgccccggcccctgcccgctccgagc -tccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgcccc -cgccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctc -cgagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgc -cccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagc -cgctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtag -ttgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg ->syndip_2_chr20:63641678-63642236 -atctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcg -ctgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcc -tcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccc -agtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccga -gctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccg-ccc -ccgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccg -ctccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgc -cctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccag -tgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagc -tccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgcccc -ctccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctc -cgagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgc -cccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagc -cgctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtag -ttgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg ->p:HG002_1_chr20:63641678-63642236 -atctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcg -ctgctggggacgcccagtaaacacgggaggagcccccgatccccaccccagctcagcgcc -tcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccc -agtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccga -gctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccg-ccc -ccgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccg -ctccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgc -cctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccag -tgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagc -tccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgcccc -ctccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctc -cgagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgc -cccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagc -cgctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtag -ttgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg ->p:HG002_2_chr20:63641678-63642236 -atctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcg -ctgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcc -tcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccc -agtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccga -gctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgcccc -ccgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccg -ctccgagctccgccccgg------------------------------------------ ------------------------------------------------------------- --------------------------------ccccgccccggcccctgcccgctccgagc -tccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgcccc -cgccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctc -cgagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgc -cccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagc -cgctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtag -ttgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg ->ref_chr20:63641678-63642236 -atctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcg -ctgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcc -tcggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccc -agtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccga -gctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-ccc -ccgcccagtgccccgccccctgactgctgctagccctgc--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------ccccgccccggcccctgcccgctccgagcttcgccccggccccgc -cccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagc -cgctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtag -ttgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgtg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d2242ccd448a7c982cfcff72641d3495.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d2242ccd448a7c982cfcff72641d3495.msa deleted file mode 100644 index 78229f17..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d2242ccd448a7c982cfcff72641d3495.msa +++ /dev/null @@ -1,250 +0,0 @@ ->syndip_1_chr20:51952383-51954992 -ctctgtctcaaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat -ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc -aaatattgatttgcttaa--ttttttttttttttgagatggggttttgctctgtcgccca -ggctggagtgcaatggcatgatcttggctcactgcaacctctgcctcctgggttcagcca -ttctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggct -aattttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtc -tcgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggc -ttgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcatt -gggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactg -ttatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcc -agacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctc -ctgagccaaggagttccagcccagcctggacaacatagtgagatcccatctctt---aaa -aaaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttctttttttttt -tttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtgg -tgtgatatcggctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagc -ctcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttt -agtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatc -cgcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcct -tccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgg -agtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctc -gtgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaattt -ttgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctggg -ctcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaag -tgcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttatt -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------aaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgat -gacttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacct -tggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggt -tggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattc -agtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtg -gttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacact -gtctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaa -agcctccttgtctctctc----tatttttttttttttttttttgaggcggagtttcgctc -ttgttggccaggctggaacgcagtgatgcgatctcggctcagtgcaacctccacctcttg -ggttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccac -catgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctg -gtctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattac -aggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagtt -tctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctctt -gggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgcca -ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc -ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat -tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt -tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactga ->syndip_2_chr20:51952383-51954992 -ctctgtctc-aaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat -ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc -aaatattgatttgcttaa-tttttttttttttttgagatggggttttgctctgtcgccca -ggctggagtgcaatggcatgatcttggctcactgcaacctctgcctcctgggttcagcca -ttctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggct -aattttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtc -tcgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggc -ttgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcatt -gggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactg -ttatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcc -agacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctc -ctgagccaaggagttccagcccagcctggacaacatagtgagatcccatctcttaaaaaa -aaaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttc--tttttttt -tttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtgg -tgtgatatcggctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagc -ctcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttt -agtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatc -cgcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcct -tccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgg -agtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctc -gtgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaattt -ttgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctggg -ctcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaag -tgcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttatt -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------aaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgat -gacttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacct -tggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggt -tggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattc -agtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtg -gttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacact -gtctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaa -agcctccttgtctctctc--tatttttttttttttttttttttgaggcggagtttcgctc -ttgttggccaggctggaacgcagtgatgcgatctcggctcagtgcaacctccacctcttg -ggttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccac -catgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctg -gtctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattac -aggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagtt -tctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctctt -gggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgcca -ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc -ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat -tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt -tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactga ->p:HG002_1_chr20:51952383-51954992 -ctctgtctc-aaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat -ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc -aaatattgatttgcttaa-tttttttttttttttgagatggggttttgctctgtcgccca -ggctggagtgcaatggcatgatcttggctcactgcaacctccgcctcctgggttcagcca -ttctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggct -aattttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtc -tcgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggc -ttgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcatt -gggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactg -ttatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcc -agacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctc -ctgagccaaggagttccagcccagcctggacaacatagtgagatcccatctcttaaaaaa -aaaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttc--tttttttt -tttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtgg -tgtgatatcagctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagc -ctcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttt -agtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatc -cgcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcct -tccttctttcctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgg -agtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctc -gtgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaattt -ttgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctggg -ctcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaag -tgcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttatt -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------aaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgat -gacttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacct -tggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggt -tggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattc -agtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtg -gttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacact -gtctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaa -agcctccttgtctctctc--tatttttttttttttttttttttgaggcggagtttcgctc -ttgttggccaggctggaacgcagtgatgcgatctcggctcagtgcaacctccacctcttg -ggttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccac -catgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctg -gtctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattac -aggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagtt -tctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctctt -gggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgcca -ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc -ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat -tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt -tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactga ->p:HG002_2_chr20:51952383-51954992 -ctctgtctcaaaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat -ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc -aaatattgatttgcttaa--ttttttttttttttgagatggggttttgctctgtcgccca -ggctggagtgcaatggcatgatcttggctcactgcaacctccgcctcctgggttcagcca -ttctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggct -aattttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtc -tcgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggc -ttgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcatt -gggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactg -ttatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcc -agacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctc -ctgagccaaggagttccagcccagcctggacaacatagtgagatcccatctctt---aaa -aaaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttctttttttttt -tttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtgg -tgtgatatcggctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagc -ctcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttc -agtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatc -cgcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcct -tccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgg -agtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctc -gtgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaattt -ttgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctggg -ctcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaag -tgcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttatt -taaaaatgcaaatccggccgggcgcggtggctcacgcctgtaatcccagcactttgggag -gccgaggcgggcggatcacgaggtcaggagatcgagaccatcccggctaaaacggtgaaa -ccccgtctctactaaaaatacaaaaaattagccgggcgtggtggcgggcgcctgtagtcc -cagctacttgggaggctgaggcaggagaatggcgtgaacccgggaggcggagcttgcagt -gagccgagatcccgccactgcactccagcctgggcgacagagcgagactccgtctcaaaa -aaaaaaaaaaaaaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgat -gacttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacct -tggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggt -tggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattc -agtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtg -gttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacact -gtctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaa -agcctccttgtctctctc----tatttttttttttttttttttgaggcggagtttcgctc -ttgttggccaggctggaatgcagtgatgcgatctcggctcagtgcaacctccacctcttg -ggttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccac -catgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctg -gtctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattac -aggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagtt -tctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctctt -gggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgcca -ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc -ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat -tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt -tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactga ->ref_chr20:51952383-51954992 -ctctgtctc-aaaaaaaaaaaagtcattgattgatctctttctggtttaactgctattat -ttagttttatagcattacattcaagtttttatagcattacaattcctagattctattttc -aaatattgatttgcttaattttttttttttttttgagatggggttttgctctgtcgccca -ggctggagtgcaatggcatgatcttggctcactgcaacctctgcctcctgggttcagcca -ttctcctgcctcagcctcccgagtggctgggactacaggtgcccgccaccacgcctggct -aattttttttttttatatttttagtagagacggggtttcaccatgttagccaggatggtc -tcgatctcctgacctcgtgatccgcccgcctcggcctcccaaagtgctaggattacaggc -ttgagccaccgcgcctggcctttaatataatttttatgaagacattatttccacttcatt -gggctctctagaattagattgcataaatactgtagttttatttcaataaaaagtcaactg -ttatttaaaccatgactaaagcttgacatgaatagagactttaaaacaataaacattgcc -agacatggtggcacatgcctgtagtctcagctactcaagaaactgagacaggaggatctc -ctgagccaaggagttccagcccagcctggacaacatagtgagatcccatctctt--aaaa -aaaaaaaaaaaaagatttgcttaattttacttttacaattttttcttttctttttttttt -tttttttttttttttttttgagatggagtcttgctctgttaccaggctggagtgcagtgg -tgtgatatcggctccctgcaacctctgcctcctgggttaaagcaattttcctgccccagc -ctcccgagtagctgggactacaggcgcgcgtcaccacacccagctaatttttgtattttt -agtagagatggggtttcaccatgttggccaggatggtctcaatctcttgatctcgtgatc -cgcccaccttggcctcccaaagtgctggaattacaggcgtgatccgccataacctggcct -tccttcttttctttaaaaatttttttctgagacagagtctcactctgttgcccagcctgg -agtgcagtggcacaatctcggctcactgtagcctccaccttctgggttcaagtgattctc -gtgcctcagcctcccgagtagctgtgactacaggtgtgtgccctcatgcctggctaattt -ttgtatttttagtagagatggggtttcaccatgttggccaggctggtctcgaaccctggg -ctcaagtgttctgtctgcctcagccccccaaagtgctgggattacaggcatgagccaaag -tgcctggctagaaaattgtaaaagtaacttaatatctgcctcatatacttttgttttatt -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------aaaaatgcaaatcctcaaccacaaatcgaaacaagaacaaccctctgat -gacttccctccctctctctttgtacaaagaagactttctgctgtctgactctgaccacct -tggtctattttatggagctccaaccctgccttgtttccttctcaggccatctgtcctggt -tggcctcactgttggaaatgctcttctcaagatgttcacgtggctggttctttgtcattc -agtctcagttcaaatactccctcctccaggaagccttccctaacttcctaggtgaaagtg -gttcccttcccctgagtcacgattatggtttcttcagtgtacttattaatggccaacact -gtctcctttattgtttgcttatgaatttaaagtctgttagcagcacctgcagcttttaaa -agcctccttgtctctctctctttttttttttttttttttttttgaggcggagtttcgctc -ttgttggccaggctggaacgcagtgatgcgatctcggctcagtgcaacctccacctcttg -ggttcaagtgattctcctgcctcagcctccttagtagctgagactacaggcatgtgccac -catgctggctaatttttgtatttttagtagagacagggtttcgtcatattggccaagctg -gtctcgaacccctgacctcaggtgatccacccatcttggcctcccagatgctgggattac -aggcgtgagccactgcgcctggcctaattgtcattttcgtttttttgttgagacagagtt -tctgtcacccaggctggaatgcagtggcacgatctcagctcactgcagcctctgcctctt -gggttcaattgattctcctgcctcagcctcccaagtagctgggactacaggtgtgtgcca -ccacacccagctaattttttcatttttagtagagacggggtttcaccatgttggtcaggc -ttgtctcgaactcctgacctcaggtgatccgtccaacttggcctcccaaagtgctgagat -tacaggcatgagctaccgtgcccagctctcaattgtcacttttagtgcatattttctggt -tgtataaaagctctcccatgcaagagggctgatgttataacagtcgattattatactgtc -ctgcattttcatcaggtaaagaaagcttttcatgtttcactga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d72a64301d60a6710fcfd33468aef027.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d72a64301d60a6710fcfd33468aef027.msa deleted file mode 100644 index 603290ea..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d72a64301d60a6710fcfd33468aef027.msa +++ /dev/null @@ -1,40 +0,0 @@ ->syndip_1_chr20:23560829-23561208 -tagtattagagtattctgaatgtcagtatgtacttagtttcactagggagatttttattc -cctaatgttcttcagcattcctttctctttctttctttctttctttctttctttccttcc -ttccttccttccttccttccttccttccttccttccttccttc----------------- ------------------------------------------------------------- -------------------------------------------ctttctttctttctttct -ttctttctttctttctttctttctttctttcttctttctttctttttcttttacagagtc -ttactcttgttgcccaggctgtagtgcagtgg ->syndip_2_chr20:23560829-23561208 -tagtattagagtattctgaatgtcagtatgtacttagtttcactagggagatttttattc -cctaatgttcttcagcattcctttctctttctttctttctttctttctttctttctttct -ttctttctttccttctttccttccttccttccttccttccttccttccttccttccttcc -ttccttccttccttctttccttctttccttctttccttctttccttctttccttctttcc -ttctttccttctttctttctttctttccttctttccttctttctttctttctttctttct -ttctttctttctttctttctttctttctttcttctttctttctttttcttttacagagtc -ttactcttgttgcccaggctgtagtgcagtgg ->p:HG002_1_chr20:23560829-23561208 -tagtattagagtattctgaatgtcagtatgtacttagtttcactagggagatttttattc -cctaatgttcttcagcattcctttctctttctttctttctttctttctttctttctttct -ttctttctttccttctttccttccttccttccttccttccttccttccttccttccttcc -ttccttctttccttctttccttctttccttctttccttctttccttctttccttctttcc -ttctttccttctttctttctttctttctttctttccttctttctttctttctttctttct -ttctttctttctttctttctttctttctttcttctttctttctttttcttttacagagtc -ttactcttgttgcccaggctgtagtgcagtgg ->p:HG002_2_chr20:23560829-23561208 -tagtattagagtattctgaatgtcagtatgtacttagtttcactagggagatttttattc -cctaatgttcttcagcattcctttctctttctttctttctttctttctttctttctttct -ttctttctttccttctttccttccttccttccttccttccttc----------------- ------------------------------------------------------------- -------------------------------------------ctttctttctttctttct -ttctttctttctttctttctttctttctttcttctttctttctttttcttttacagagtc -ttactcttgttgcccaggctgtagtgcagtgg ->ref_chr20:23560829-23561208 -tagtattagagtattctgaatgtcagtatgtacttagtttcactagggagatttttattc -cctaatgttcttcagcattcctttctctttctttctttctttctttctttctttctttct -ttctttctttccttctttccttccttccttccttccttccttccttccttccttccttcc -ttccttccttccttctttccttctttccttctttccttctttccttctttccttctttcc -ttctttcc------------ttctttccttctttccttctttctttctttctttctttct -ttctttctttctttctttctttctttctttcttctttctttctttttcttttacagagtc -ttactcttgttgcccaggctgtagtgcagtgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d758d8d416dd205a6f2a3a988afe6ca4.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d758d8d416dd205a6f2a3a988afe6ca4.msa deleted file mode 100644 index e5a411fe..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d758d8d416dd205a6f2a3a988afe6ca4.msa +++ /dev/null @@ -1,65 +0,0 @@ ->syndip_1_chr20:62830512-62830938 -cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag -gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta -cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- -----------------------ccccaccacagtcccccaccccccaccccagtccccaa -acccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccca -ccccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa -cccccatgacagtccctca--------------------acccccaccacagtcccccaa -cccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccacc -ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca-c -ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa -tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcc ->syndip_2_chr20:62830512-62830938 -cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag -gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta -cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca -aacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccca -acccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcca -acccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa -cccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaa -cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc -ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc -ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa -tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcc ->p:HG002_1_chr20:62830512-62830938 -cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag -gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta -cccatgtaccacagtcccccaccccccaccacagtcccccaccccccaccccagtcccca -aacccctaccacagtcccccaaccccaccacagtcccccaccccctaccacagtccccca -acccctaccacagtcccccaacccccaccacagtcccccaccccc-accacagtccgcca -acccccatgacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa -cccccatgacagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaa -cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc -ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc -ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa -tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcc ->p:HG002_2_chr20:62830512-62830938 -cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag -gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta -cccatgtaccacagtcccccaccccccaccgtgctccacc-------------------- -----------------------ccccaccacagtcccccaccccccaccccagtccccaa -acccctaccacagtcccccaa-ccccaccacagtcccccaccccctaccacagtccccca -ccccctaccacagtcccccaacccccaccacagtcccccacccccaccacagtccgccaa -cccccatgacagtccctca--------------------acccccaccacagtcccccaa -cccccatgacagtcccccaacccccaccacagtcccccaacccccaccacagtccccacc -ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatccccca-c -ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa -tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcc ->ref_chr20:62830512-62830938 -cccagggccagaagggcagcatgggagaccccggccttccaggcccccagggcctccgag -gtgacgtgggcgaccgggtaagtggccctctcagcaggaagctcccctgcaccccctcta -cccatgtaccacagtccccc---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------acccccatgacagtcccccaa -cccccaccacagtcccccaacccctaccacagtcccccaacccccaccacagtccccacc -ccctaccacagtcccccaacccccaccacagtcccccaccccctaccacaatcccccacc -ccccaccacagtcccctgggacgcagacagggagaggcccttgcagctcccagtgggaaa -tctggccatgggcagtgtctccctgcgtggcggaggcagtggcatcagggccccgactgt -ggcgcctttggcccctctgaccttcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_d7a2f60d1de438a8e90fb28960164bac.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_d7a2f60d1de438a8e90fb28960164bac.msa deleted file mode 100644 index 0ef978fb..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_d7a2f60d1de438a8e90fb28960164bac.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:63221399-63221831 -catctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaag -gtggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgca -gggattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggact -gcagggattgcagggattgcagggactgcagggactgca--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------ttgctcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgc -aggctctgctacaaga ->syndip_2_chr20:63221399-63221831 -catctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaag -gtggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgca -gggattgcagggactgcagggattgcagggattgcagggagtgcagggactgcagggact -gcagggattgcagggactgcagggactgcagggactgcagggactgcagggactgcaggg -actgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgca -gggactgcagggattgcagggactgcagggactgcagggactgcagggactgcagggact -gcagggattgcagggattgcagggattgcagggactgcagggattgcagggactgcaggg -actgcagggattgcagggactgcagggactgcagggactgcagggattgcagggattgca -gggattgcagggattgcagggattgcagggactgcagggactgcagggactgcagggact -gcagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcaggg -attgcagggattgcagggattgcagggattgcagggattgcagggattgcagggactgca -gggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggact -gcagggactgcagggattgcagggattgcagggattgcagggattgcagggactgcaggg -actgcattgctcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgc -aggctctgctacaaga ->p:HG002_1_chr20:63221399-63221831 -catctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaag -gtggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgca -gggattgcagggactgcagggattgcagggattgcagggattgcagggactgcagggatt -gcagggactgcagggactgcagggactgcagggactgcagggactgcagggattgcaggg -attgcagggattgcagggactgcagggactgcagggattgcagggattgcagggactgca -gggactgcagggattgcagggactgcagggactgcagggactgcagggactgcagggact -gcagggactgcagggattgcagggattgcagggattgcagggattgcagggactgcaggg -actgcagggactgcagggactgcagggactgcagggactgcagggattgcagggattgca -gggattgcagggattgcagggattgcagggactgcagggactgcagggactgcagggact -gcagggattgcagggattgcagggattgcagggattgcagggactgcagggactgcaggg -attgcagggattgcagggattgcagggattgcagggattgcagggattgcagggactgca -gggactgcagggactgcagggattgcagggattgcagggactgcagggactgcagggatt -gcagggactgcagggactgcagggactgcagggattgcagggattgcagggactgcaggg -actgcattgctcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgc -aggctctgctacaaga ->p:HG002_2_chr20:63221399-63221831 -catctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaag -gtggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgca -gggattgcagggactgcagggactgcagggattgcagggactgcagggactgcagggact -gcagggattgcagggattgcagggactgcagggactgca--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------ttgctcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgc -aggctctgctacaaga ->ref_chr20:63221399-63221831 -catctgcctgtaagtaccagtgccaggtgctctggggccgatgtctccgttagccccaag -gtggaggctcagggagcagatgtgagcgtgccttgctcatcgcagtagcttcggactgca -gggattgcagggactgcagggattgcagggattgcagggattgcagggactgcagggatt -gcagggactgcagggactgcagggactgcagggactgcagggactgcagggattgcaggg -attgcagggattgcagggactgcagggattgcagggactgcagggactgcagggattgca -gggactgcagggactgcagggactgcagggattgcagggattgcagggactgcagggact -gca--------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------ttgctcttgcagcaccacccgcctccgtggacaccttcagcagtgagacaatgc -aggctctgctacaaga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_da3b0c9819e644da5199a38fe7d7aca1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_da3b0c9819e644da5199a38fe7d7aca1.msa deleted file mode 100644 index 7ce0683a..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_da3b0c9819e644da5199a38fe7d7aca1.msa +++ /dev/null @@ -1,190 +0,0 @@ ->syndip_1_chr20:63948484-63948763 -agagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctc -ggtgtgaggagggaggcgtgtgtgagagggaggggatgtgtgtgagaggga-ggggcgtg -tgtgagagggaggggcgtgtgtgaggg---aggggtgtgtgtgagagggaggggcgtgtg -tgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtga-ggggcgtgtgtga -gagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgtgagagg -taggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagaggg--- ---------------aggggcgtgtgtgtgagggaggggcgtgtgagag-ggagggggcgt -gtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtgag -agggagggggcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt----ggga -gggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagacggag -gggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggg -gcgtgtgtgagggagggg---gcgtgtgagagggaggggcgtgtgtgagagggagggggc -gtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt -gtgagagggaggggcgtgtgagaggg-aggggcgtgtgtgagagg----------gaggg -ggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggc -gtgtgtgagagggagggggcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgt -gagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtga -gagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagag-- -------ggagggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtga -gaggga-ggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagg -gagggggcgtgtgtgagagggagggggcgtgt-------------gtgagagggagaggc -gtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggagaggcgtgt -gtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgt -gagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag -agggagaggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagg -gaggggcgtgtgtgagagggag--------------ggggcgtgtgtgagagggaggggc -gtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga-ggggcg -tgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcgtgtgt -gagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtg-----agagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagg -ggcgtgtgtgagagggaaggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg -cgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggg-gcgt -gtgagagggaggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcgtgtgtg -agaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgagaggg -agggggcgtgtgtgagggaggggcgtgtgtgagagggaggggggcgtgtgtgagagggag -ggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaagggaggggg -tgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcact ->syndip_2_chr20:63948484-63948763 -agagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctc -ggtgtgaggagggaggcgtgtgtgagagggaggggatgtgtgtgagagggagggggcgtg -tgtgagagggaggggcgtgtgtgagag---aggggtgtgtgtgagagggaggggcgtgtg -tgagagggagggggcgtgtgtgaaagggaggggcgtgtgtgaggga-ggggcgtgtgtga -gagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgtgagagg -gaggggcgtgtgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgagggggggc -gtgtgtgagagggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggaggggcgt -gtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag --gggggggcgtgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtgagaggga -gggggcgtgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga---aggg -aggggtgtgtgtgagagtgggggcgtgtgtgagaggg--------gcgtgagaggtaggg -gcgtgtgtgagagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga-ggggc -gtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt -gtgagagggaggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtgaggggg -ggcgtgtgtgagaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-agggaggggc -gtgtgtgagaggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggcgtgtgt -gagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtga -gagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgaggggggc -gtgtgagagggaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgtgtgtga -gagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaag -ggaggggtgtgtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggtaggggc -gtgtgtgagagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgt -gtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgt -gagggagggggcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag --ggagggggcgtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgtgagagg -caggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtga---gggggggc -gtgtgtgagaggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcg -tgtgtgagagggaggggcgtgtgtgagggagggggcgtgt-------------------- ------------gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-agggagg -ggcgtgtgtgagagtg--ggggcgtgtgtgagaggg--------gcgtgagaggtagggg -cgtgtgtgagagggagggg-gcgtgagagggaggggcgtgtgtgagagggaggggcgtgt -gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtg -agagggagggggcgtgtgtgagagggaggggcgtgt---------------gtgagaggg -aaggggcgtgtgagagggaggggcgtgtgtgagaggaaggggcgtgtgtgaga---ggga -ggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaagggaggggg -tgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcact ->p:HG002_1_chr20:63948484-63948763 -agagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctc -ggtgtgaggagggaggcgtgtgtgagagggaggggatgtgtgtgagagggagggggcgtg -tgtgagagggaggggcgtgtgtgagag---aggggtgtgtgtgagagggaggggcgtgtg -tgagagggagggggcgtgtgtgaaagggaggggcgtgtgtgaggga-ggggcgtgtgtga -gagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggagggggcgtgtgtgagagg -gaggggcgtgtgtgagaggcaggggcgtgtgtgagagtgggggcgtgtgtgagggggggc -gtgtgtgagagggagggggcgtgtgtgagaggtaggggcgtgtgtgagagggaggggcgt -gtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgag --gggggggcgtgtgtgagagggagggggcgtgtgagagggaggggcgtgtgtgagaggga -gggggcgtgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgtgtga---aggg -aggggtgtgtgtgagagtgggggcgtgtgtgagaggg--------gcgtgagaggtaggg -gcgtgtgtgagagggaggggtgtgtgtgagagggaggggcgtgtgtgagaggga-ggggc -gtgtgtgag-ggagggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt -gtgagagggaggggcgtgtgtgagagtgggggcgtgtgtgggggggcgtgtgtgaggggg -ggcgtgtgtgagaggta-ggggcgtgtgtgagagggaggggcgtgtgtg-agggaggggc -gtgtgtgagaggcaggggcgtgtgtgggggggggcgtgtgt--gaggggggggcgtgtgt -gagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtga -gagggaggggcgtgtgtgagaggcaggggcgtgtgtggggggggcgtgtgtgaggggggc -gtgtgagagggaggggcgtgtgtggggaggggcgtgtgtgagagggaggggcgtgtgtga -gagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgaag -ggaggggtgtgtgtgagagtgggggcgtgtgtgagagttaggggcgtgagaggtaggggc -gtgtgtgagagggaggggcgtgtgtgaggga-ggggcgtgtgtgagagggaggggcgtgt -gtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgt -gagggagggggcgtgtgcgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag --ggagggggcgtgtgtgagagggaggggcgtgtgagag-ggagggggcgtgtgtgagagg -caggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtga---gggggggc -gtgtgtgagaggtaggggcgtgtgtgagagggagggggcgtgtgtgagagggagggggcg -tgtgtgagagggaggggcgtgtgtgagggagggggcgtgt-------------------- ------------gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtga-agggagg -ggcgtgtgtgagagtg--ggggcgtgtgtgagaggg--------gcgtgagaggtagggg -cgtgtgtgagagggagggg-gcgtgagagggaggggcgtgtgtgagagggaggggcgtgt -gtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagaggcaggggcgtgtgtg -agagggagggggcgtgtgtgagagggaggggcgtgt---------------gtgagaggg -aaggggcgtgtgagagggaggggcgtgtgtgagaggaaggggcgtgtgtgaga---ggga -ggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaagggaggggg -tgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcact ->p:HG002_2_chr20:63948484-63948763 -agagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctc -ggtgtgaggagggaggcgtgtgtgagagggaggggatgtgtgtgagagggagggggcgtg -tgtgagagggaggggcgtgtgtgag-----aggggtgtgtgtgagagggaggggcgtgtg -tgagagggagggggcgtgtgtgagaggcagggg-gcgtgtgtgtga-ggggcgtgtgtga -gagggaggggcgtgtgtgagagggagggg-gcgtgtgtgagggggggcgtgtgtgagagg -taggggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagaggg--- ---------------aggggcgtgtgtgtgagggaggggcgtgtgagag-ggagggggcgt -gtgtgagaggcaggggcgtgtgtgtgagggaggggcgtgagagggaggggcgtgtgtgag -agggagggggcgtgtgtgagggggggcgtgtgtgagaggtaggggcgtgtgt----ggga -gggggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagacggag -gggcgtgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggg -gcgtgtgtgagggagggg---gcgtgtgagagggaggggcgtgtgtgagagggagggggc -gtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgtgagggagggggcgtgt -gtgagagggaggggcgtgtgagaggg-aggggcgtgtgtgagagg----------gaggg -ggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgaagggaggggc -gtgtgtgagagggagggggcgtgagagggaggggcgtgtgtgagagggaggggcgtgtgt -gagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtga -gagggaggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagag-- -------ggagggggcgtgtgagagggagggggcgtgtgtgagagggagaggcgtgtgtga -gaggga-ggggcgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagg -gagggggcgtgtgtgagagggagggggcgtgt-------------gtgagagggagaggc -gtgtgtgagagggaggggcgtgtgtgagggagggggcgtgtgtgagagggagaggcgtgt -gtgagagggagggggcgtgtgtgagagggagaggcgtgtgtgagagggaggggcgtgtgt -gagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgag -agggagaggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgtgtgagagg -gaggggcgtgtgtgagagggag--------------ggggcgtgtgtgagagggaggggc -gtgtgtgagagggaggggcgtgtgtgagagggagggggcgtgtgtgagaggga-ggggcg -tgtgtgagagggaggggcgtgtgtgaagggaggggcgtgtgtgagagtgggggcgtgtgt -gagttaggggcgtgagaggtaggggcgtgtgtgagagggaggggcgtgtgtgagagggag -ggggcgtg-----agagggaggggcgtgtgtgagagggaggggcgtgtgtgagagggagg -ggcgtgtgtgagagggagggggcgtgtgtgagagggaggggcgtgtgtgagagggagggg -cgtgtgtgagaggcaggggcgtgtgtgagggaggggcgtgtgtgagagggagggg-gcgt -gtgagagggaggggcgtgtgtgagagggaggggc--gtgtgagagggaggggcgtgtgtg -agaggga-ggggcgtgtgtgagagggaggggcgtgtgtgagagggaggggcgtgagaggg -agggggcgtgtgtgaggaaggggcgtgtgtgagagggaggggggcgtgtgtgagagggag -ggggcgtgtgtgagagggagggggtgtgtgtgagaccgagggggcgtgtaagggaggggg -tgtgtgtgagagggaagcgtgtgcacacaccagccctaaccatgatcact ->ref_chr20:63948484-63948763 -agagatgattccatctgtataaaatccaggaaacgaaggacgctcaccgccatgcgcctc -ggtgtgaggagggaggcgtgtgtgagagggaggggatgtgtgtgagagggagggggcgtg -tgtgagagggaggggcgtgtgtgagagggaaggggcgtgtgtgagagggaggggcgtgtg -tgagagggagggggtgtgtgtgagaccgagggg-gcgtgtaagggagggggtgtgtgtga -gagggaagcgtgtgcaca------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------caccagccctaaccatgatcact diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_da9e583f8bb0c9329678fe2798c29f69.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_da9e583f8bb0c9329678fe2798c29f69.msa deleted file mode 100644 index 518d1963..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_da9e583f8bb0c9329678fe2798c29f69.msa +++ /dev/null @@ -1,125 +0,0 @@ ->syndip_1_chr20:63028776-63029502 -caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg -agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca -aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc -cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccggg -cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg -ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccc -cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcc -cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggt -cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag -gtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgc -aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgt -gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt -gtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctcc -gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct -ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc -gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg -ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt -catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca ->syndip_2_chr20:63028776-63029502 -caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg -agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca -aa---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------cgcac -ccga-------------------------------------------------------- ------------------------------------------------------------- ---------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct -ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctcc -gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg -ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt -catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca ->p:HG002_1_chr20:63028776-63029502 -caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg -agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca -aa---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------cgcac -ccga-------------------------------------------------------- ------------------------------------------------------------- ---------gtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct -ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcccccgggcctcc -gcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgtctccgtgtgcaggtcccccgggcccctgcgtctctgtgtgcaggctcaagtttg -ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt -catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca ->p:HG002_2_chr20:63028776-63029502 -caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg -agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca -aacgcacccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcg -cctccgtgtgcaggtcccccgggcctccgcctctccgtgtgcaggtcccccgggcctccg -cgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctc -cgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcc -tccgcgtctgtgtgtgcaggtcccccgggcctccgcgtctgcgtgtgcaggtcccccggg -cctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccg -ggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccc -cgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctccgtgtgcaggtcc -cccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggt -cccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcag -gtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctccgtgtgc -aggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgt -gcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgtctgtgt -gtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctcc -gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct -ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctcc -gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgcctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg -ccaacgtccatgcacgtctcagcctctcagcctggactggacaactcggcttcgggaatt -catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgaattca ->ref_chr20:63028776-63029502 -caacaatgcacaagtggcttgagtagaagagctgctcctgctgggaggcgcaggaggctg -agcgaggcccaccctgcaggggcgaggccacggtttgtgttatttcccatgatgactcca -aa---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------cgcac -ccgagtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcctccgt -gtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctccgcgcctcc -gtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgcct -ccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgcgc -ctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcctccgc -gcctccgtgtgcaggtcccccgggcctccgcgtctgtgtgtgcaggtcccccgggcctcc -gcgcctccgtgtgcaggtcccccgggcctccgcgcctccgtgtgcaggtcccccgggcct -ccgcgtctccgtgtgcaggtcccccgggcctctgcgtctctgtgtgcaggctcaagtttg -ccaacgtccatgcacgtctcagcctctcagcctggactggacaactgggcttcgggaatt -catttaaattctacccgctacacgccttccctggattcagggcggcgtccagtgcattca diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb507ec4de0d55fd44561115d512b4c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb507ec4de0d55fd44561115d512b4c.msa deleted file mode 100644 index d1f1f4b4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb507ec4de0d55fd44561115d512b4c.msa +++ /dev/null @@ -1,60 +0,0 @@ ->syndip_1_chr20:49834009-49834658 -gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg -tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta -atattagcttgtctctctctctctctctctctctctctctctctctctctctctc----- --------tatatatatatatatatacacacacacacacactatgtatatacacacactgt -atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat -acagtgtgtatatatatatatactgtgtgtatatatatatatactgtata---------- ---------------------tatatatatatatactgtgtatatatatatactg------ ----------------------------------------tgtatatatatatatatactg -tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg -aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa ->syndip_2_chr20:49834009-49834658 -gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg -tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta -atattagcttgtctctctctctctctctctctctctctctctctctctctctctctctct -ctctatatatatatatatatatatatatacacacacacactatgtatatacacacactgt -atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat -acagtgtgtatatatatatatactgtgtatatatatatatactgtatatatatatatact -gtgtatatatatatatactgtatatatatatatactgtgtatatatatatactgtatata -tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg -tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg -aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa ->p:HG002_1_chr20:49834009-49834658 -gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg -tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta -atattagcttgtctctctctctctctctctctctctctctctctctctctctctctctct -ctctatatatatatatatatatatatatacacacacacactatgtatatacacacactgt -atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat -acagtgtgtatatatatatatactgtgtatatatatatatactgtatatatatatatact -gtgtatatatatatatactgtatatatatatatactgtgtatatatatatactgtatata -tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg -tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg -aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa ->p:HG002_2_chr20:49834009-49834658 -gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg -tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta -atattagcttgtctctctctctctctctctctctctctctctctctctctctctc----- --------tatatatatatatatatacacacacacacacactatgtatatacacacactgt -atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat -acagtgtgtatatatatatatactgtgtgtatatatatatatactgtata---------- ---------------------tatatatatatatactgtgtatatatatatactg------ ----------------------------------------tgtatatatatatatatactg -tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg -aaatacattcattttctctgttgggtagattgatttgacctaactttgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa ->ref_chr20:49834009-49834658 -gaggctgagacaggcggatcacctgaggttgggagttcaagaccagcttggccaacatgg -tgaaactctgtctctgctaaaaatacaaaaattagccgggcgtggtggtgcacgcttgta -atattagcttg--tctctctctctctctctctctctctctctctctctctctctctctct -atatatatatatatatatatatatatatacacacacacactatgtatatacacacactgt -atatacgcactatatgcactatatatacacacagtatatgtatatacacacactatatat -acagtgtgtatatatatatatactgtgtatatatatatatactgtatatatatatatact -gtgtatatatatatatactgtgtatatatatatactgtgtatatatatatactgtatata -tatactgtatatatatatatatactgtatatatatatactgtgtatatatatatatactg -tatatatacacacacacactatatatatgccatatataatatctggtggccagttgtgtg -aaatacattcattttctctgttgggtagattgatttgacctaactatgagcctcaatctc -aagaggtaaagtggtagtttgccaatttaatgctgcacaaaggattatttaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb6122dabcdfbfdfd1b60aa0d3cffd6.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb6122dabcdfbfdfd1b60aa0d3cffd6.msa deleted file mode 100644 index 818a0ba0..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ddb6122dabcdfbfdfd1b60aa0d3cffd6.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:62360090-62360812 -aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca -gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt -gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca -gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg -atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc -aggcagagggatgggataggataggtgggtgggtgggtggatagggagggggtggggtgg -gtgcataggtaggggggtggatgggtcagcaggcagcgggatgggataggataggtgggt -gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtgggtgggta -gaaggataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaata -gatgggtgggtgggtgggtgggtggatggataggtgggtgggtgggtggagggatagatg -ggtgggtggatgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgg -gtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgggtgg -gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg -gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg -agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag ->syndip_2_chr20:62360090-62360812 -aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca -gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt -gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca -gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg -atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc -aggcaga----------------------------------------------------- --------------------------------------gggatgggataggataggtgggt -gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtggagggata -----------------------------------------gatgggtgggtgggtagaag -gataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaatagatg -ggtg-------------------------------------------------------- ----------------------------ggtgggtgggtgggtggatggataggtgggtgg -gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg -gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg -agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag ->p:HG002_1_chr20:62360090-62360812 -aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca -gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt -gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca -gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg -atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc -aggcaga----------------------------------------------------- --------------------------------------gggatgggataggataggtgggt -gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtggagggata -----------------------------------------gatgggtgggtgggtagaag -gataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaatagatg -ggtg-------------------------------------------------------- ----------------------------ggtgggtgggtgggtggatggataggtgggtgg -gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg -gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg -agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag ->p:HG002_2_chr20:62360090-62360812 -aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca -gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt -gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca -gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg -atggatgggtagggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc -aggcagagggatgggataggataggtgggtgggtgggtggatagggagggggtggggtgg -gtgcataggtaggggggtggatgggtcagcaggcagcgggatgggataggataggtgggt -gggtggagggatagatgggtggtgggtgggtggagggatagatgggtgggtgggtgggta -gaaggataggtaggtgggtgggtgggtggatggataggtggatgggtgggtggaggaata -gatgggtgggtgggtgggtgggtggatggataggtgggtgggtgggtggagggatagatg -ggtgggtggatgggtgggtggagggatagatgggtggtgggtgggtggagggatagatgg -gtgggtgggtgggtagaaggataggtaggtgggtgggtgggtggatggataggtgggtgg -gtgggtggaggaata--------gatgggtgggtggatgggtgggtggagggatagatgg -gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg -agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag ->ref_chr20:62360090-62360812 -aaggacatttccccaccccactccagggagtccctgcccccaccctgaccaaggctggca -gccccctggcctaggccgagacaggggccttggtagatacatccacgtggtcaggaaagt -gggtgagaaggaaggaagacggtgcaggtgtggagggaggaatgagcagacaggtggaca -gatggatggaaacaaggaataaagggtgggtgctgcataggtaggggggtgggtgggtgg -atggatgggta-ggggtgggtgggtggatacgttgggggtgggtgggtgggtgggtcagc -aggcaga----------------------------------------------------- --------------------------------------gggatgggataggataggtgggt -gggtggagggatgggtg---agtgggtgggtggagggatagatgggtgg----------- -------------------------------------------tgggtgggtggagggata -gatgggt-ggtgggtgggtggagggatagatgggtgggtgggtgggtggagggatagatg -ggt--------------------------------------------------------- ----------------------------ggtgggtgggtggagggatagatgggtggatgg -gtgggtagaaggataggtaggtgggtgggtgggtggatgggtgggtggagggatagatgg -gtgggtgggtgggtggagggatagatgggtgggtgggtggagggaccacttcccaggtgg -agtggaaagggttcctcttccctccgtatcattttacagttggtgaaactgaggctgtga -gaggcaagacgctcacatggcggaacctgatttctggcccagaacaatctaaaag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e595ac0692ae672cf3ea7a03e1e6ad6c.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e595ac0692ae672cf3ea7a03e1e6ad6c.msa deleted file mode 100644 index eaecc408..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e595ac0692ae672cf3ea7a03e1e6ad6c.msa +++ /dev/null @@ -1,180 +0,0 @@ ->syndip_1_chr20:63964668-63966717 -cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc -aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg -aggag------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------caccctgacc -tggaacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccata -ccttttctcaccactgttcctccccgacctgggacgagcccccataccttttctcaccac -tgt---tccctgacctgggacgagcccccataccttttcttaccactgttcctccctgtg -gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt -ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg -actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta -atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt -ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg -actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag -actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt -ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg -atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctggg ->syndip_2_chr20:63964668-63966717 -cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc -aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg -aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg -ggacaagcccccataccttttcttaccactgttccctgacctgggacgagcccccatacc -ttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttc -cccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagc -ccccataccttttctcaccactgttcctccccgacctgggacgagcccccataccttttc -tcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctga -cctggaacgagcccccataccttttctcaccactgttccccgacctgggacgagccccca -taccttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccact -gttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggac -gagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctttt -ctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttccccg -acctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccccc -ataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttcttac -cactgttcctccccaacctgggacgagcccccataccttttctcaccactgttcctcccc -gacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccc -cataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctta -ccactgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccc -cgacctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccc -ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttcttacc -actgttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacc -tgggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccata -ccttttcttaccactgttcctccctgacctgggacgagcccccataccttttcttaccac -tgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccctgtg -gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt -ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg -actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta -atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt -ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg -actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag -actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt -ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg -atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctggg ->p:HG002_1_chr20:63964668-63966717 -cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc -aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg -aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg -ggacaagcccccataccttttcttaccactgttccctgacctgggacgagcccccatacc -ttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttc -cccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagc -ccccataccttttctcaccactgttcctccccgacctgggacgagcccccataccttttc -tcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctga -cctggaacgagcccccataccttttctcaccactgttccccgacctgggacgagccccca -taccttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccact -gttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggac -gagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctttt -ctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttccccg -acctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccccc -ataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttcttac -cactgttcctccccaacctgggacgagcccccataccttttctcaccactgttcctcccc -gacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccc -cataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctta -ccactgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccc -cgacctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccc -ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttcttacc -actgttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacc -tgggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccata -ccttttcttaccactgttcctccctgacctgggacgagcccccataccttttcttaccac -tgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccctgtg -gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt -ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg -actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta -atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt -ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg -actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag -actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt -ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg -atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctggg ->p:HG002_2_chr20:63964668-63966717 -cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc -aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg -aggag------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------caccctgacc -tggaacgagcccccataccttttctcaccactgttccctgacctgggacgagcccccata -ccttttctcaccactgttcctccccgacctgggacgagcccccataccttttctcaccac -tgt---tccctgacctgggacgagcccccataccttttcttaccactgttcctccctgtg -gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt -ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg -actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgtgaccgta -atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt -ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg -actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag -actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt -ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg -atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctggg ->ref_chr20:63964668-63966717 -cctggcctgcttgggtggaattgggcaggtgtccaggctgtccgcagccctgcagggagc -aggtgaggtgagggccaggagggcctaactgtgggccccattacccccaggccgtggccg -aggagcaccctgacctggaacgagcccccataccttttctcaccactgttccccgacctg -ggacaagcccccataccttttcttaccactgttccctgacctgggacgagcccccatacc -ttttctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttc -cccgacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagc -ccccataccttttctcaccactgttcctccccgacctgggacgagcccccataccttttc -tcaccactgttccccgacctgggacgagcccccataccttttctcaccactgttccctga -cctggaacgagcccccataccttttctcaccactgttccccgacctgggacgagccccca -taccttttctcaccactgttccccgacctgggacgagcccccataccttttctcaccact -gttccccgacctgggacgagcccccataccttttctcaccactgttccccgacctgggac -gagcccccataccttttctcaccactgttccccgacctgggacgagcccccatacctttt -ctcaccactgttccctgacctgggacgagcccccataccttttctcaccactgttccccg -acctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccccc -ataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctcac -cactgttcctccccaacctgggacgagcccccataccttttctcaccactgttcctcccc -gacctgggacgagcccccataccttttctcaccactgttccctgacctgggacgagcccc -cataccttttcttaccactgttcctccccgacctgggacgagcccccataccttttctta -ccactgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccc -cgacctgggacgagcccccataccttttcttaccactgttccccgacctgggacgagccc -ccataccttttctcaccactgttccctgacctgggacgagcccccataccttttcttacc -actgttccctgacctgggacgagcccccataccttttctcaccactgttcctccccgacc -tgggacgagcccccataccttttctcaccactgttccccgacctgggacgagcccccata -ccttttcttaccactgttcctccctgacctgggacgagcccccataccttttcttaccac -tgttcctccccgacctgggacgagcccccataccttttcttaccactgttcctccctgtg -gcacgaggtgctttgttctccgacctggtcagcagcaccattttgcagggcggtgtgtgt -ctgctgatagcaatgggcctgctgactgtcaccggcttgctgaccacaatgggcctgctg -actgtcactggcttggtgaccggcacgggtttcgtaactgtcacaagctttgttaccgta -atgggtttggtgacaggtacgggtttggtgaccggcacagacttggtgactgtgatgggt -ttggtgaccggcatggccttggtgacgggcatgggcctgctgactgtgacaggtttggtg -actggcacgggcctagtgaccgggatggccttggtgactggcatgggtctgccgaccgag -actggcttgctgatgccaatgggtttgctgacacccacaggtttgccaatagtgacaggt -ttgctcactccgatgggcttgctgaccccaacaggccggctgatggtgaccggcctgctg -atgggcccaggcttggaggcaggcaggggtcggtccatgtggttccagatccggtgtttc -tccagctggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e61bd325b5ef9f5c7d4241bdb738d3f9.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e61bd325b5ef9f5c7d4241bdb738d3f9.msa deleted file mode 100644 index 02ef8da2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e61bd325b5ef9f5c7d4241bdb738d3f9.msa +++ /dev/null @@ -1,190 +0,0 @@ ->syndip_1_chr20:20337099-20337808 -ttacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagag -gaagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctca -ctagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtgga -tggatggatggatggatggatggatggatagatgggtgggtggatggatggatggataga -tgggtggatggatagatgggtggatggataaatggatggatggatggatggatagatggg -tgggtggatggatggatggatggatggatggatggatggatggatagatggatagatggg -tgggtggatggatggatggatggatggatggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatgga -tggatagatgtgtgggtggatggatggatggatggatggatggatggatggatggataga -tggatagatgggtgggtggatggatggatggatggatggatggatggatggatggataga -tgggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggg -tggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgt -tcttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgt -ttacaatcctgcctgcctctcacccagacctcttg ->syndip_2_chr20:20337099-20337808 -ttacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagag -gaagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctca -ctagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtgga -tggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtggatggataaatggatgg----atggatggatggatagatgggtgggtgga -tggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatgga -tggatagatgggtgggtggatggatggatggatggatggatggatagatggataga---- -------------tgggtgggtggatggatggatggatggatggatggatggatggataga -tgggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtggg----tggatggatggatggatggatggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggata--------------------gatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggataga-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------tgggtgggtgggtggatggatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggg -tggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgt -tcttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgt -ttacaatcctgcctgcctctcacccagacctcttg ->p:HG002_1_chr20:20337099-20337808 -ttacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagag -gaagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctca -ctagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtgga -tggatggatggatggatggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtggatggataaatggatgg----atggatggatggatagatgggtgggtgga -tggatggatggatggatggatggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatggatggatggatggatggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatgga -tggatagatgggtgggtggatggatggatggatggatggatggatagatggataga---- -------------tgggtgggtggatggatggatggatggatggatggatggatggataga -tgggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtggg----tggatggatggatggatggatggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggata--------------------gatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggataga-------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------tgggtgggtgggtggatggatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggg -tggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgt -tcttagcagacgtcccaccatggaagaggtcatggggcacaggggctttgggaaaggtgt -ttacaatcctgcctccctctcacccagacctcttg ->p:HG002_2_chr20:20337099-20337808 -ttacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagag -gaagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctca -ctagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtgga -tggatggatggatggatggatggatggatagatgggtgggtggatggatggatggataga -tgggtggatggatagatgggtggatggataaatggatggatggatggatggatagatggg -tgggtggatggatggatggatggatggatggatggatggatggatagatggatagatggg -tgggtggatggatggatggatggatggatggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatgggtggatggataaatggatggatggatgga -tggatagatgtgtgggtggatggatggatggatggatggatggatggatggatggataga -tggatagatgggtgggtggatggatggatggatggatggatggatggatggatggataga -tgggtggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatggatagatgggtgggtggatggatggatggataga -tgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatgggtgggtggatggatggatggatggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatggatggatggatgga -tggatggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtgga -tggatggatggatagatggatagatgggtgggtggatggatggatggatagatggataga -tgggtgggtggatggatggatggatagatgggtgggtggatggatggatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatggatagatggg -tgggtggatggatggatggatagatgggtgggtggatggatggatggatggatggataga -tggatagatgggtgggtggatggatggatggatagatgggtgggtggatggatggatgga -tggatggatggatggatggatggatagatggatagatgggtgggtggatggatggatgga -tagatgggtgggtggatggatggatggatagatggatagatgggtgggtggatggatgga -tggatagatggatagatgggtgggtggatggatggatggatagatgggtgggtggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatggatagatgggtggg -tggatggatggatggatagatgggtgggtggatggatggatggatagatgggtgggtggg -tggatggatggatggatggatggatagaataaaaagaaagctaggacatggttctagtgt -tcttagcagacgtcccaccatggaagaggtcatggggcacaggggctttgggaaaggtgt -ttacaatcctgcctccctctcacccagacctcttg ->ref_chr20:20337099-20337808 -ttacgtggaagcatagggaaggaagggatgtttgttgaggggtggtgtgatgcagcagag -gaagaggaccagaggaaagcagccactggaaataaggaaacagggtttaggaaggcctca -ctagacctgttaggatggatgcatggatggatggatggatggacagaatgggtgggtgga -tggatggatggatagatggatggatggatggatggatggatggatggatggatggatgga -tagatgggtgggtgg----gtggatgg----atggatggatggatggatggatggatgga -tggatggatagatgggtgggtggatggatggatggatagatggatagatgggtgggtgga -tggatggatggatagatgggtgggtggatggatggatggatagatgggtggatggataaa -tggatggatggatggatggatagatgggtgggtggatggatggatggatggatggatgga -tggatggatagat------------------gtgggtggatggatggatggatagatggg -tgggtgggtggatggatggatggatggatagatgggtgggtgggtggatggatggatgga -tggatagaataaaaaagaaa---------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------gctaggacatggttctagtgt -tcttagcagacgtcccaccatggaagaggtcatggagcacaggggctttgggaaaggtgt -ttacaatcctgcctgcctctcacccagacctcttg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e6d049b50ef2cdc3dada615791cd0988.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e6d049b50ef2cdc3dada615791cd0988.msa deleted file mode 100644 index b3051f77..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e6d049b50ef2cdc3dada615791cd0988.msa +++ /dev/null @@ -1,110 +0,0 @@ ->syndip_1_chr20:38123689-38124113 -ataatatgtataataataatatataatatttataataataatatatataatatgtatata -taatatacatatacctattatatataatatacctattatatataatatacatatacctat -tatatataatatacctattatatataagatacctattatatataatatacatatacctat -tatatatataatatacct----------------attatatat-------atataatata -cctattatatatataatatacctat--tatatatataatatacctattatatatataata -tacctattatatatataatatacctat--tatatataatatacctattatatataa---- ----aatatacctattatatataatatacctattatatacattatatataatatacctatt -atatgcattatatataatat---acctattatatgcattatatataatatacctattata -tgcattatatataatatacctattatatgcattatatataatatacctattatatgcatt -atataatatattatatataatatgcatattatatgtattatatattatatattatatata -taatatacatattatatgtattatatattatatattatatatataatatacatattatat -gtattatatattatatataatatacatattatatattatatattatatacatattatata -ttatatattatatacatattatatattatatacatattatatattatatattatatacat -attatacattatatatatctaaaatatataatacacattatatattatataatacacatt -atatataatatataatacacattatatattatatataatacacattatatattatatata -atacacattatatat-----------------------tatataatacacattatatatt -atatataatacacattatatattatatataatacacattatatattatatataatacaca -ttatatattatataatacacattatatattatatataatacacattatatatataataca -cattatatattatatataatacataatacacattatatattatatataatacacattata -tataatatataacacacattatatataatatataacacacattatatattatatataata -cacattatatattatatataatacaca ->syndip_2_chr20:38123689-38124113 -ataatatgtataataataatatataatatttataataataatatatataatatgtatata -taatatacatatacctattatatataatatacctattatatataatatacatatacctat -tatatataatatacctattatatataagatacctattatatataatatacatatacctat -tatatatataatatacct----------------attatatat-------atataatata -cctattatatatataatatacctat--tatatatataatatacctattatatatataata -tacctattatatatataatatacctat--tatatataatatacctattatatataa---- ----aatatacctattatatataatatacctattatata---------------------- ------cattatatataatat---acctattatatgcattatatataatatacctattata -tgcattatatataatatacctattatatgcattatatataatatacctattatatgcatt -atataatatattatatataatatgcatattatatgtattatatattatatattatatata -taatatacatattatatgtattatatattatatattatatatataatatacatattatat -gtattatatattatatataatatacatattatatattatatattatatacatattatata -ttatatattatatacatattatatattatatacatattatatattatatattatatacat -attatacattatatatatctaaaatatataatacacattatatattatataatacacatt -atatataatatataatacacattatatattatatataatacacattatatattatatata -atacacattatatattatataatacacattatatattatatataatacacattatatatt -atatataatacacattatatattatatataatacacattatatattatatataatacaca -ttatatattatataatacacattatatattatatataatacacattatatatataataca -cattatatattatatataatacataatacacattatatattatatataatacacattata -tataatatataacacacattatatataatatataacacacattatatattatatataata -cacattatatattatatataatacaca ->p:HG002_1_chr20:38123689-38124113 -ataatatgtataataataatatataatatttataataataatatatataatatgtatata -taatatacatatacctattatatataatatacctattatatataatatacataaacctat -tatatataatatacctattatatataagatacctattatatataatatacctatacctat -tatatatataagatacct----------------attatatataatatacatacctatta -cctattatatatataatatacctattatatatatataatatacctattatatatataata -tacctat-----------tatacctat--tatatataatatacctattatatatat---- ----aatatacctattatatataatatacctattatata---------------------- ------cattatatataatat---acctattatatgcattatatataatatacctattata -tgcattatatataatatacctattatatgcattatatataatatacctattatatgcatt -atataatatattatatataatatgcatattatatgtattatatattatatattatatata -taatatacatattatatgtattatatattatatattatatatataatatacatattatat -gtattatatattatatataatatacatattatatattatatattatatacatattatata -ttatatattatatacatattatatattatatacatattatatattatatattatatacat -attatacattatatatatctaaaatatataatacacattatatattatataatacacatt -atatataatatataatacacattatatattatatataatacacattatatattatatata -atacacattatatattatataatacacattatatattatatataatacacattatatatt -atatataatacacattatatattatatataatacacattatatattatatataatacaca -ttatatattatataatacacattatatattatatataatacacattatatatataataca -cattatatattatatataatacataatacacattatatattatatataatacacattata -tataatatataacacacattatatataatatataacacacattatatattatatataata -cacattatatattatatataatacaca ->p:HG002_2_chr20:38123689-38124113 -ataatatgtataataataatatataatatttataataataatatatataatatgtatata -taatatacatatacctattatatataatatacctattatatataatatacataaacctat -tatatataatatacctattatatataagatacctattatatataatatacctatacctat -tatatatataatataccttatatataagatacctattatatataatatacata-----ta -cctattatatatataatatacctattatatatatataatatacctattatatatataata -tacctattatatatataatatacctat--tatatatataatacctattatatataatata -cctattatatacattatatataatatacctattatatg---------------------- ------cattatatataatat---acctattatatgcattatatataatatacctattata -tgcattatatataatatacctattatatgcattatatataatatacctattatatgcatt -atataatatattatatataatatgcatattatatgtattatatattatatattatatata -taatatacatattatatgtattatatattatatattatatatataatatacatattatat -gtattatatattatatataatatacatattatatattatatattatatacatattatata -ttatatattatatacatattatatattatatacatattatatattatatattatatacat -attatacattatatatatctaaaatatataatacacattatatattatataatacacatt -atatataatatataatacacattatatattatatataatacacattatatattatatata -atacacattatatat-----------------------tatataatacacattatatatt -atatataatacacattatatattatatataatacacattatatattatatataatacaca -ttatatattatataatacacattatatattatatataatacacattatatatataataca -cattatatattatatataatacataatacacattacctattatatataatacacattata -tataatatataacacacattatatataatatataacacacattatatattatatataata -cacattatatattatatataatacaca ->ref_chr20:38123689-38124113 -ataatatgtataataataatatataatatttataataataatatatataatatgtatata -taatatacatatacctattatatataatatacctattatatataatatacataaacctat -tatatataatatacctattatatataagatacctattatatataatatacctat------ ---tatatataagatacct----------------attatatataatatacata-----ta -cctattatatatataatatacctattatatatatataatatacctattatatatataata -tacctattatatatataatatacctattatatatataatatacctattatatataa---- --------tacacattatatataata----tataacaca---------------------- ------cattatatataatatataacacacattatatattatatataatacacat----ta -tatattatatataatacac----------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------a diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e6d60a69339bd27d991f56bee3548e38.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e6d60a69339bd27d991f56bee3548e38.msa deleted file mode 100644 index 874331ac..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e6d60a69339bd27d991f56bee3548e38.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:61289552-61290383 -ctggggagtgtgaccacaggccagtggcagtccctgcctttggattaaagagccctttga -ggcttgcttggtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgta -tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg -tatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccc -cgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtt -tatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctg -ggtttatcccgatatccaatgagacttgctggatttatccccgtatccaa---------- ----------------------------------------------------- ->syndip_2_chr20:61289552-61290383 -ctggggagtgtgaccacaggccagtggcagtccctgcctttggattaaagagccctttga -ggcttgcttggtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgta -tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg -tatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccc -cgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtt -tatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctg -ggtttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgc -tggatttatccccgtatccaa------------------------------- ->p:HG002_1_chr20:61289552-61290383 -ctggggagtgtgaccacaggccagtggcagtccctgcctttggattaaagagccctttga -ggcttgcttggtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgta -tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg -tatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccc -cgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtt -tatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctg -ggtttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgc -tggatttatccccgtatccaa------------------------------- ->p:HG002_2_chr20:61289552-61290383 -ctggggagtgtgaccacaggccagtggcagtccctgcctttggattaaagagccctttga -ggcttgcttggtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgta -tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg -tatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccc -cgtatccaacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtt -tatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctg -ggtttatcccgatatccaatgagacttgctggatttatccccgtatccaa---------- ----------------------------------------------------- ->ref_chr20:61289552-61290383 -ctggggagtgtgaccacaggccagtggcagtccctgcctttggattaaagagccctttga -ggcttgcttggtgatgtcatggaaaacagcatatgacaccaagatatccccatatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgta -tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg -tatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccc -cgtatccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtt -tatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg -gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc -tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaa diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e7315f7330dde260068b31e9e14647d0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e7315f7330dde260068b31e9e14647d0.msa deleted file mode 100644 index 7b2e62c3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e7315f7330dde260068b31e9e14647d0.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:53203887-53204573 -cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt -aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc -cttcatttttataatatgatactattatatcataattttataatatactattatatcata -ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat -atactattatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgat---atactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat -gatgatatgatactatatcatcacatgatgatatg--atactatatcatcacatgatgat -atgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatact -atatcatc---------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------acatgatgatatgatactat -atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact -atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata -ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga -tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt -tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctatt ->syndip_2_chr20:53203887-53204573 -cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt -aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc -cttcatttttataatatgatactattatatcataattttataatatactattatatcata -ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatg--atactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcataacatgatgatatgatactatatcataacatgatgatatgatactatatca -tcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactatat -catcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactat -atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact -atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata -ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga -tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt -tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctatt ->p:HG002_1_chr20:53203887-53204573 -cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt -aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc -cttcatttttataatatgatactattatatcataattttataatatactattatatcata -ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatat -gatgatatgatactatatcatcatatgatgatatg--atactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcataacatgatgatatgatactatatcataacatgatgatatgatactatatca -tcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactatat -catcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactat -atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact -atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata -ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga -tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt -tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctatt ->p:HG002_2_chr20:53203887-53204573 -cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt -aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc -cttcatttttataatatgatactattatatcataattttataatatactattatatcata -ttatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatgat -atactattatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatcatatgatgat---atactatatcatcatatgatgatatgatactatatcatc -atatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatg -atatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgata -ctatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatca -tcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatga -tgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatga -tactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatat -catcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcacat -gatgatatgatactatatcatcacatgatgatatg--atactatatcatcacatgatgat -atgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatact -atatcatc---------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------acatgatgatatgatactat -atcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatact -atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata -ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga -tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt -tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctatt ->ref_chr20:53203887-53204573 -cataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactgt -aagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatctc -cttcatttttataatatgatactattatatcataattttataatatactattatatcata -ttatatgatactatttatatcatcatatgatgatatgat--------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------atactatatcatcatatgatgatatgatatactatatcatcatatgatgat -atgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatact -atatcatc---------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------------atatgatgatatgatactat -atcatcat-----atgatgatatgatactatatcatcatataacatgatgatatgatact -atatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgata -ctatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatga -tactattatatcataatatgatataatattttggacatactaggttaaataagatatagt -tatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatatg -aaattccatgcatagctgacattctacttctatt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_e98e8b7a2d661c3ba62b21a0dbc4f7d7.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_e98e8b7a2d661c3ba62b21a0dbc4f7d7.msa deleted file mode 100644 index 26a82542..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_e98e8b7a2d661c3ba62b21a0dbc4f7d7.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:45600469-45600846 -aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc -atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt -gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt -aaaagcagtctctctctctctctctctctctctctctctctctctctatccccccctccc -tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc -tctctctctctccctctctctctctttctccctctctctccctctctctctctctctctc -cctctctctctctttctccctctctctccctctctccccctctctctccctctctccctc -tctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact -tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgg ->syndip_2_chr20:45600469-45600846 -aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc -atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt -gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt -aaaagcagtctctctctctctctctctctctctct--ctctctctctatccccccctccc -tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc -tctctctctctccctctctct--------------------------------------- --------------------------------------ccctctctccccctctctctccc -tctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact -tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgg ->p:HG002_1_chr20:45600469-45600846 -aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc -atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt -gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt -aaaagcagtctctctctctctctctctctctctct--ctctctctctatccccccctccc -tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc -tctctctctctccctctctct--------------------------------------- --------------------------------------ccctctctccccctctctctccc -tctctccctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact -tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgg ->p:HG002_2_chr20:45600469-45600846 -aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc -atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt -gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt -aaaagcagtctctctctctctctctctctctctctctctctctctctatccccccctccc -tccctccttccctccctccctctctctctctctctccctttctctgtctctccctctctc -tctctctctctccctctctctctctttctccctctctctccctctctctctctctctctc -cctctctctctctttctccctctctctccctctctccccctctctctccctctctccctc -tctccctctctctccctctctctctacccctgaatctggcctttctaaacaccctcaact -tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgg ->ref_chr20:45600469-45600846 -aatattgggaattttactgatggtaaaattaaaataggaggaggaggttacatcactatc -atatggtaacattcccttaaaaatcatctctttatctttcctaaatattccactgtcttt -gactgctatacctctctctcttttctttcaccaagcctctctctttgctttccttctggt -aaaagcagtctctctctctctctctctctctctct------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------ctc -tatccccccctctccctctctctctacccctgaatctggcctttctaaacaccctcaact -tgtgtacctgtatactatactgagctacactaaagtttctatatttagccaaatccagcc -catcataccagctcttcccctggtatattcctaggagtgg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ea32b528f5bf011c6688fcdb99f4cdbb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ea32b528f5bf011c6688fcdb99f4cdbb.msa deleted file mode 100644 index 04b11f70..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ea32b528f5bf011c6688fcdb99f4cdbb.msa +++ /dev/null @@ -1,295 +0,0 @@ ->syndip_1_chr20:62057472-62059240 -ctccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttga -gatcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggg -acacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtcta -cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -cgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggaca -caggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctc -aggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaac -ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg -ctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcc -acagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtc -tacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagg -acggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaa -gacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagaca -atggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacaca -ccaggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacgga -cacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaa -cctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggg -gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg -ccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacagg -tctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagga -aggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctca -gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg -gacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcca -acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg -ggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccag -gccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacg----------------------------------------------------- ---------------------gacacaggtctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctc------------------------------------------------ --------------------------ggggggccaacctctccagtccccaaacacagtcc -ccaacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccct -cacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagc -tgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggc -aggcctggagaagagcctgggaccaccgcggactgacc ->syndip_2_chr20:62057472-62059240 -ctccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttga -gatcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggg -acacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctc----------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctca------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------gcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcca -acctcagcaagacctcaggaaggacggacacaggt------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctca -gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctc------------------------------------------------ ---------------------------gggggccaacctctccagtccccaaacacagtcc -ccaacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcctgccct -cacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagc -tgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggc -aggcctggagaagagcctgggaccaccgcggactgacc ->p:HG002_1_chr20:62057472-62059240 -ctccaagatccatgtaccccaacaccaccctacctggccacgctcctctcacaactttga -gatcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggg -acacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctc----------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------------gggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctca------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------gcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcca -acctcagcaagacctcaggaaggacggacacaggt------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----ctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctca -gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctc------------------------------------------------ ---------------------------gggggccaacctctccagtccccaaacacagtcc -ccaacagacaacttctcctgtcctcacatgcggctcccaacaaacaatttctcctgccct -cacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagc -tgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggc -aggcctggagaagagcctgggaccaccgcggactgacc ->p:HG002_2_chr20:62057472-62059240 -ctccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttga -gatcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggg -acacaaagggcccagcaagacctcaggaaggacggacacaggtctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtcta -cacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggac -ggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaag -acctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -cgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacac -caggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggaca -caggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctc -aggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaac -ctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatgggg -ctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggcc -acagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtc -tacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagg -acggacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaa -gacctcaggaaggacggacacaggcctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagaca -atggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacaca -ccaggccacagacagtggggctcggggggccaacctcagcaagacctcaggaaggacgga -cacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacct -caggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggggccaa -cctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaatggg -gctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccagg -ccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacagg -tctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctcagga -aggacggacacaggcctacacaccaggccacagacaatggggctcggggggccaacctca -gcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacag -acaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctac -acaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacg -gacacaggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcca -acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg -ggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccag -gccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacaca -ggtctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacg----------------------------------------------------- ---------------------gacacaggtctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctc------------------------------------------------ --------------------------ggggggccaacctctccagtccccaaacacagtcc -ccaacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccct -cacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagc -tgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggc -aggcctggagaagagcctgggaccaccgcggactgacc ->ref_chr20:62057472-62059240 -ctccaagatccatgtaccccaacaccaccctacctggctacgctcctctcacaactttga -gatcaagatgccacgtgtgccttcctcacatcggcgctttccagtgatgcccagtggggg -acacaaagggcccagcaagacctcaggaaggacggacacaggcctacacaccaggccaca -gacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggccta -cacaccaggccacagacaatggggctcg-------------------------------- ------------------------------------------------------------- -------------------------------------------------------gggggc -caacctcagcaagacctcaggaaggacggacacaggcctacacaccaggccacagacaat -ggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggtctacacacc -aggccacagacaatggggctcgggggccaacctcagcaagacctcaggaaggacggacac -aggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaagacctca -ggaaggacggacacaggcctacacaccaggccacagacaatggggctcgggggccaacct -cagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggct -cgggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccac -agacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcct -acacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcaggaagga -cggacacaggtctacacaccaggccacagacaatggggctcggggggccaacctcagcaa -gacctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcggggg -gccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagaca -atggggctcgggggccaacctca------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------gcaagac -ctcaggaaggacggacacaggtctacacaccaggccacagacaatggggctcgggggcca -acctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacagacaatgg -ggctcggggggccaacctcagcaagacctcaggaaggacggacacaggcctacacaccag -gccacagacaatggggctcggggggccaacctcagcaagacctcaggaaggacggacaca -ggcctacacaccaggccacagacaatggggctcgggggccaacctcagcaagacctcagg -aaggacg----------------------------------------------------- ---------------------gacacaggtctacacaccaggccacagacaatggggctcg -ggggccaacctcagcaagacctcaggaaggacggacacaggtctacacaccaggccacag -acaatggggctcgggggccaacctcagcaagacctcaggaaggacggacacaggtctaca -caccaggccacagacaatggggctcggggggccaacctctccagtccccaaacacagtcc -ccaacagacaacttctcctgtccccacatgcggctcccaacaaacaatttctcctgccct -cacacgcggttcccaacgacaacttctgctccacaacatgacacccacggtgggagaagc -tgggggcacttcactacatcatcctgcacactgcagcatggcctgctccaggcagaaggc -aggcctggagaagagcctgggaccaccgcggactgacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ed1042b42c059891aecf75a626d0d1a8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ed1042b42c059891aecf75a626d0d1a8.msa deleted file mode 100644 index 9504a597..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ed1042b42c059891aecf75a626d0d1a8.msa +++ /dev/null @@ -1,195 +0,0 @@ ->syndip_1_chr20:55943819-55945907 -gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc -caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca -gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat -cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta -aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg -ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac -cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata -tatatagatacacacacacacacacacacacacac------------------------- ----------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc -agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg -tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa -aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg -agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc -cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta -tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt -tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata -tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata -gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt -tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag -tatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctagat -atct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag -atatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc -tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata -tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc -tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc -gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta -tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag -atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct -atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag -atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct -atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct -gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat -ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt -ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt -ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact -gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag -gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tggg ->syndip_2_chr20:55943819-55945907 -gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc -caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca -gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat -cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta -aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg -ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac -cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata -tatatagatacacacacacacacacacacacacacacacacacacacacacacacatata -tatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgc -agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg -tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa -aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg -agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc -cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta -tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt -tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata -tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata -gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt -tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag -tatctatctagatatcgg--------------------tctagatagtatctatctagat -atctgcgtagatgtctagatatctatctagatat---------------tatctatctag -a----------------------------------------------------------- -----------------------------------------tatctgtcgctatctagata -tctatctaga---tatctgtcgctatctagatatctatctaga----------------- -----------------------------------------------------tatctgtc -gctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatca -tctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatctatctag -atatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatct -atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag -atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct -atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct -gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat -ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt -ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt -ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact -gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag -gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tggg ->p:HG002_1_chr20:55943819-55945907 -gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc -caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca -gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat -cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta -aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg -ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac -cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata -tatatagatacacacacacacacacacacacacacacacacacacacacacacacatata -tatatatatatatatatatatatatatatatatatatatatatgcatgcatgccagatgc -agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg -tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa -aattagctggctgtggtggctcatgctggtaattccagctacttgggaggctgaggcagg -agaatcacatgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc -cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta -tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt -tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata -tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata -gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt -tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag -tatctatctagatatcgg--------------------tctagatagtatctatctagat -atctgcgtagatgtctagatatctatctagatat---------------tatctatctag -a----------------------------------------------------------- -----------------------------------------tatctgtcgctatctagata -tctatctaga---tatctgtcgctatctagatatctatctaga----------------- -----------------------------------------------------tatctgtc -gctatctagatatctatctagatatcatctgtcgctatctagatatctatctagatatca -tctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatctatctag -atatcatctgtcgctatctagatatctatctagatatcatctgtcgctatctagatatct -atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag -atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct -atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct -gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat -ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt -ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt -ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact -gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag -gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tggg ->p:HG002_2_chr20:55943819-55945907 -gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc -caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca -gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat -cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta -aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg -ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac -cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata -tatatagatacacacacacacacacacacacacac------------------------- ----------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc -agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg -tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa -aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg -agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc -cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta -tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt -tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata -tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata -gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt -tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag -tatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctagat -atct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag -atatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatc -tagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagata -tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc -tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc -gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta -tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag -atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct -atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag -atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct -atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct -gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat -ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt -ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt -ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact -gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag -gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tggg ->ref_chr20:55943819-55945907 -gtgctgggtactgtcccagtcctcctacctgtttacctcacttccacccttgcctccttc -caagtcaatcccatgggaaccagcattttctgaaactcaataaaattagctagcatttca -gccaggtgcagtggctcaagcctgtaatcccagcactttgggaggccaaggtgggtggat -cacttgaggttaggagtttgagaccagcctggccaacatggtgaaacctcgcctctacta -aaaatacaaaaattagctgggcatgctggcatgtgcctgtaatcccagctactcaggagg -ctgaggcaggagaactgcttgagcctgggaggcagaggttgcagtgagctgagatggcac -cactgcattccagctgggcaacagagagagactctttcttaaatatatatattttatata -tatatagatacacacacacacacacacacacacac------------------------- ----------atatatatatatatatatatatatatatatatatgcatgcatgccagatgc -agtggctcacgcctgtaatcccagcactttgagaggccaaggtgggcagatcatctgagg -tcaggagttccagaccagcctagccaacatggtgaaactccatctctactaaaaatacaa -aattagctggctgtggtggctcatgctggtaatcccagctacttgggaggctgaggcagg -agaatcacttgaacctgggaggtggaggttgcagtgagccgagatcacaccactgcactc -cagcctggatgacagagcgagactccattaaaaaaatatatctatatctatagatatcta -tagatatatatctagatatagatctatgagtatatatctatagatatctagatatatatt -tatagatagatatatctatagatatctatatatttctatcgatagagatatctatagata -tctatcaatatatctatagatttctagagatatgtatctagatataaatctatagacata -gatatagatatatagatatttaactgccaatgtcctaaacactttatactcaacacattt -tttataaaaaaaaatagatatcggtctagatagtatctatctagatatcggtctagatag -tatctatctagatatctgtgtagatgtctagatatctatctagatattatctatctagat -atct--gtcgctatctagatatctatctagatatctgtcgctatctagatatctatctag -a----------------------------------------------------------- -----------------------------------------tatctgtcgctatctagata -tctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatc -tagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtc -gctatctagatatctatctagatagtatctgtcgctatctagatatctatctagatagta -tctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatctatctag -atagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctagatatct -atctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgctatctag -atatctatctagatagtatctgtcgctatctagatatctatctagatagtatctgtcgct -atctagatatctatctagatagtatctgtcgctatctagatatctatctagatagtatct -gtcgctatctagatatctatctagatagtatctgtcgctatctagatatctagatagtat -ctgtcgctatctagatatctagatagtatctgtctagatagctatctagatagtatctgt -ctagatagctatctagatagtatctgtccagatatctgtagctatctagattgtatctgt -ctagatatctgtagatatctagatatctatatctatctggatatctatagatatttaact -gccgggcaatgtcctaaaccctttacactcaacacatttcattttataacaaaatatgag -gtagatattattatttccctcaactcacagagaagaaaaaaatgaagcatatggagccca -tggg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ed11e856d3a32487f771047b0b77f027.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ed11e856d3a32487f771047b0b77f027.msa deleted file mode 100644 index 156d29b9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ed11e856d3a32487f771047b0b77f027.msa +++ /dev/null @@ -1,155 +0,0 @@ ->syndip_1_chr20:20320185-20320679 -atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat -ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga -tggtatttcagatatatag--atatatatattatatatatgtaatatatataatatatgt -a--atatattatatatatgtaatatatataatatatgtaatatattatatatatgtaata -tatataatatatgtaatatatattatatatgtaatatatataatatatgtaatatatatt -atatatgtaatatatataatatatgtaatatatattatatatgtaatatataatatatgt -aatatatattatatatgtaatataatatatgtaatatatattatatatgtaatatatatt -acatatattatatatgcaatatatattatatatattatatatgcaatatatattatatat -attatatatgcaatatatattatatatgcaatatatattatatatattatatatgcaata -tatattatatatattacatatgtaatatatattacatatgtaatatataatatattatat -attacatatgtaatatataatatattatatattacatatgtaatatataatatatattac -atatgtaatatataatatatattacatatgtaatatattatatattacatatgtaatata -ttatatattacatatgtaatatattatatattacatatgtaatatattatatattacata -tgtaatatattatatattacatatgtaatatatataatatattacatatgtaatatataa -tatattatatatgtaatatatattacatatataatatatataatatatatgtaatatatt -atatatattatatatgtaatatatattacatatataatatatattatatatattacatat -attatatatgtaatatatattacatatgtaatatatgtaatatatattacatatgtaata -tatattatatatgtaatatatattacatatattatatatgtaatatatattatatatatt -atatatgtaatgtataatatatatattatatatgtaatatatattatatataatatatgt -aatatatattatatatgtaatgtatattatatatattatatatgtaatgtatattatata -taatatatgtaatgtatattatatatgtaatatatattatgtatattatatatgtaatat -atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta -tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata -ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat -atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa -tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata -ttatatatattatatatgtaatatatattatatatattatatatgtaatatatattatat -atattatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacat -actgaagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactg ->syndip_2_chr20:20320185-20320679 -atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat -ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga -tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt -aatatatattatatatatgtaatatatataatatatgta---------atatatgtaata -tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat -atatgta----atatataatatatgtaatatatattatatatgtaatatataatatatat -tatatatgtaatatatatatatttaaaaacagaaccattatctttta-gagatacatact -gaagtgtctggagacatgcttcaagata-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------acccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactg ->p:HG002_1_chr20:20320185-20320679 -atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat -ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga -tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt -aatatatattatatatatgtaatatatataatatatgta---------atatatgtaata -tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat -atatgta----atatataatatatgtaatatatattatatatgtaatatataatatatat -tatatatgtaatatatatatatttaaaaacagaaccattatctttta-gagatacatact -gaagtgtctggagacatgcttcaagata-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------acccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactg ->p:HG002_2_chr20:20320185-20320679 -atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat -ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga -tggtatttcagatatatag--atatatatattatatatatgtaatatatataatatatgt -a--atatattatatatatgtaatatatataatatatgtaatatattatatatatgtaata -tatataatatatgtaatatatattatatatgtaatatatataatatatgtaatatatatt -atatatgtaatatatataatatatgtaatatatattatatatgtaatatataatatatgt -aatatatattatatatgtaatataatatatgtaatatatattatatatgtaatatatatt -acatatattatatatgcaatatatattatatatattatatatgcaatatatattatatat -attatatatgcaatatatattatatatgcaatatatattatatatattatatatgcaata -tatattatatatattacatatgtaatatatattacatatgtaatatataatatattatat -attacatatgtaatatataatatattatatattacatatgtaatatataatatatattac -atatgtaatatataatatatattacatatgtaatatattatatattacatatgtaatata -ttatatattacatatgtaatatattatatattacatatgtaatatattatatattacata -tgtaatatattatatattacatatgtaatatatataatatattacatatgtaatatataa -tatattatatatgtaatatatattacatatataatatatataatatatatgtaatatatt -atatatattatatatgtaatatatattacatatataatatatattatatatattacatat -attatatatgtaatatatattacatatgtaatatatgtaatatatattacatatgtaata -tatattatatatgtaatatatattacatatattatatatgtaatatatattatatatatt -atatatgtaatgtataatatatatattatatatgtaatatatattatatataatatatgt -aatatatattatatatgtaatgtatattatatatattatatatgtaatgtatattatata -taatatatgtaatgtatattatatatgtaatatatattatgtatattatatatgtaatat -atattatatatattatatatgtaatatatattatatatattatatatgtaatatatatta -tatatattatatatgtaatatatattatatatattatatatgtaatatatattatatata -ttatatatgtaatatatattatatatattatatatgtaatatatattatatatattatat -atgtaatatatattatatatattatatatgtaatatatattatatatattatatatgtaa -tatatattatatatattatatatgtaatatatattatatatattatatatgtaatatata -ttatatatattatatatgtaatatatattatatatattatatatgtaatatatattatat -atattatatatgtaatatatatatatttaaaaacagaaccattatcttttagagatacat -actgaagtgtctggagacatgcttcaagataacccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactg ->ref_chr20:20320185-20320679 -atcctgattcagataaactgttaaacaaaaatctgtgccatttatgaggtgattggaaat -ttgaaacctggagagttaatgatgataagcaattatgattaatttttttagcagtaaaga -tggtatttcagatatatagatatatatatattatatatatgtaatatatataatatatgt -aatatatattatatatatgtaatatatataatatatgta---------atatatgtaata -tatattatatatgtaatata----atatatgtaatatatattatatatgtaatatataat -atatgta----atatataatatatgtaatatatattatatatgtaatatataatatatat -tatatatgtaatatatatatatttaaaaacagaaccattatctttta-gagatacatact -gaagtgtctggagacatgcttcaagata-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------acccaggagggagaatggtagaaggaact -agagatgacccaagactgcccttgagctaataactg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_edce4871de28f10080aaa834a9139704.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_edce4871de28f10080aaa834a9139704.msa deleted file mode 100644 index dca76d89..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_edce4871de28f10080aaa834a9139704.msa +++ /dev/null @@ -1,90 +0,0 @@ ->syndip_1_chr20:62270179-62271194 -cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca -gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc -tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg -ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc -tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg -gtcctctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctcct -tgtc-----------------------------cctctctgggtcctctccttgtccctc -tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg -gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg -tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc -tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt -gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt -ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc -tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtggga ->syndip_2_chr20:62270179-62271194 -cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca -gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc -tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg -ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc -tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg -gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct -ctccttgtccctc-ctgg-----------------------cctctctgggtcctctcct -tgtc-------------------------------------------------------- ----------------------------------------------------cctctctgg -gtcctctccttgtccctctctgacctctctgggtcctctccttgtccctctctgggtcct -ctccttgtc-----------------------------------------cctctctggg -tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc -tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt -gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt -ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc -tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtggga ->p:HG002_1_chr20:62270179-62271194 -cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca -gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc -tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg -ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc -tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg -gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct -ctccttgtccctc-ctgg-----------------------cctctctgggtcctctcct -tgtc-------------------------------------------------------- ----------------------------------------------------cctctctgg -gtcctctccttgtccctctctgacctctctgggtcctctccttgtccctctctgggtcct -ctccttgtc-----------------------------------------cctctctggg -tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc -tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt -gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt -ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc -tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtggga ->p:HG002_2_chr20:62270179-62271194 -cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca -gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc -tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg -ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc -tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg -gtcctctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctct---gacctctctgagtcctctcct -tgtc-----------------------------cctctctgggtcctctccttgtccctc -tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg -gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg -tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc -tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt -gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt -ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc -tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtgaga ->ref_chr20:62270179-62271194 -cgtcctagtccctggtgcagacgaggagcctgagaggcttagcagctcatgtgtgtgtca -gctgggaacccacagcaagtggattccaaagcctgccatgtccctgttgccactagcacc -tcctcctccactccctcctggcctctctgggtcctctccttgtccctcctggcctctctg -ggtcctctccttgtccctccctgacctctctgggtcctctccttgtccctctctggcctc -tctgggtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgg -gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct -ctccttgtccctc-ctggcctctctgggtcctctccttgtccctctctgggtcctctcct -tgtccctctctggcctctctgggtcctctctgacctctctgggtcctctccttgtccctc -tctgggtcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgg -gtcctctccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcct -ctccttgtccctctctggcctctctgggtcctctccttgtccctctctggcctctctggg -tcctctccttgtccctctctgggtcctctccttgtccctctctggcctctctgggtcctc -tccttgtccctctctggcctctctgggtcctctccttgtccctctctgggtcctctcctt -gtccctctctggcctctctgggtcctctccttgtccctctctggcctctctgggtccttt -ccttgtccctttctggtctctctggtcctctccttctctccttgtccctctccctctgcc -tctgctttgcccaccccagaccctgctccttcctgaagagcctgccctgaggtgacagct -gtgtttccctggaatgcctactgcccttgggatccctttcctggaagcccggtggga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f012a5688bdbef469c3e125fa60771eb.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f012a5688bdbef469c3e125fa60771eb.msa deleted file mode 100644 index cdc65394..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f012a5688bdbef469c3e125fa60771eb.msa +++ /dev/null @@ -1,115 +0,0 @@ ->syndip_1_chr20:48449684-48450495 -agtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtgga -gcatgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatgg -gatgggatg-----ggatggatggatgggatggatggatgggatgggataggatggatgg -ggtgagatgggatggaatggatgggatgggatggatggatgggatgggatggatgggatg -ggatggatgggatgggatggatgggatggatgggatggaatgggatggatgggatgggat -gggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggat -ggatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatg -gatgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatg -gggtgggatgagatggatgggatggatgggatgggatggatggatggatgggatgggatg -gatggatgggatgggatgggatggggt------------------------ggatgggat -ggatggatggatgggatgggatggatggatgggatgggatggat-gaatgggatgtgatg -gatgggatggaatgggat-agatgggatgggattggatgggatggggtgggatggggtaa -gatggggtgggatgggatggtatgggatggatggatgagatgggatgggatgagatggga -ttggatggggtgggatgcaatgggatgagatgagatgagatgagatgggatggatggcat -gggatgggatgggattggatggggtgggatgggatggggtaggatgggatgggatgggat -gggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatggggt -gggttgggatggggtggggtgggatgggatgggatgggatggggtggggtggggtggggt -gggatggggtgggatggggtgggatgggatggggtgggatgggatgggatggggtgggat -gggatggggtggggtggggtggggtgggatgaggtggggtgggatgggatgggatggggt -ggggtggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgggat -gcgatgggatgagatgagatggatggcatgggatgggtgggaggggatgggatattatca -gatggcaaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcat ->syndip_2_chr20:48449684-48450495 -agtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtgga -gcatgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatgg -gatgggatg-------------ggatgggatggatggatgggatgggataggatggatgg -ggtgagatgggatggaatggatgggatgggatggatggatgggatgggatggatgggatg -ggatggatgggatgggatggatgggatggatgggatggaatgggatggatgggatgggat -gggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggat -ggatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatg -gatgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatg -gggtgggatgagatggatgggatggatgggatgggatggatggatggatgggatgggatg -gatggatgggatgggatgggat-ggatggatgggatgggatgggatggggtggatgggat -ggatggatggatgggatgggatggatggatgggatgggatggat-gaatgggatgtgatg -gatgggatggaatgggat-agatgggatgggattggatgggatggggtgggatggggtaa -gatggggtgggatgggatggtatgggatggatggatgagatgggatgggatgagatggga -ttggatggggtgggatgcaatgggatgagatgagatgagatgagatgggatggatggcat -gggatggaatgggattggatggggtgggatgggatggggtaggatgggatgggatgggat -gggatgggatgggatggggtgggatgggttgggatgggatggggtgggttgggatggggt -ggggtgggatgggatgggatggggtgggatggggtgggatggggtgggatggggtgggat -gggatggggtgggatgggatgggatgggatggggtgggatggggtggga-----tgggat -ggggtggggtggggtggggtgggatgaggtggggtgggatgggatgggatggggtggggt -ggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgggatgcgat -gggatgagatgagatgagatggatggcatgggatgggtgggaggggatgggatattatca -gatggcaaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcat ->p:HG002_1_chr20:48449684-48450495 -agtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtgga -gcatgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatgg -gatgggatg-------------ggatgggatggatggatgggatgggataggatggatgg -ggtgagatgggatggaatggatgggatgggatggatggatgggatgggatggatgggatg -ggatggatgggatgggatggatgggatggatgggatggaatgggatggatgggatgggat -gggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggat -ggatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatg -gatgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatg -gggtgggatgagatggatgggatggatgggatgggatggatggatggatgggatgggatg -gatggatgggatgggatgggatggggtggatgggatgga--tggatggatgggatgggat -ggatggatggatgggatgggatggatggatgggatggaatggat-gaatgggatgtgatg -gatgggatggaatgggat-agatgggatgggattggatgggatggggtgggatggggtaa -gatggggtgggatgggatggtatgggatggatggatgagatgggatgggatgagatggga -ttggatggggtgggatgcaatgggatgagatgagatgagatgagatgggatggatggcat -gggatggaatgggattggatggggtgggatgggatggggtaggatgggatgggatgggat -gggatgggatgggatggggtgggatgggttgggatgggatggggtgggttgggatggggt -ggggtgggatgggatgggatggggtgggatggggtgggatggggtgggatggggtgggat -gggatggggtgggatgggatgggatgggatggggtgggatggggtggga-----tgggat -ggggtggggtggggtggggtgggatgaggtggggatgggatggatgggatgggatggggt -ggggtggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgggat -gcgatgggatgagatgagatggatggcatgggatgggtgggaggggatgggatattatca -gatggcaaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcat ->p:HG002_2_chr20:48449684-48450495 -agtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtgga -gcatgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatgg -gatgggatg-----ggatggatggatgggatggatggatgggatgggataggatggatgg -ggtgagatgggatggaatggatgggatgggatggatggatgggatgggatggatgggatg -ggatggatgggatgggatggatgggatggatgggatggaatgggatggatgggatgggat -gggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggat -ggatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatg -gatgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatg -gggtgggatgagatggatgggatggatgggatgggatggatggatggatgggatgggatg -gatggatgggatgggatgggatggggt------------------------ggatgggat -ggatggatggatgggatgggatggatggatgggatgggatggat-gaatgggatgtgatg -gatgggatggaatgggat-agatgggatgggattggatgggatggggtgggatggggtaa -gatggggtgggatgggatggtatgggatggatggatgagatgggatgggatgagatggga -ttggatggggtgggatgcaatgggatgagatgagatgagatgagatgggatggatggcat -gggatgggatgggattggatggggtgggatgggatggggtaggatgggatgggatgggat -gggatgggatgggatgggatgggatgggatggggtgggatgggttgggatgggatggggt -gggttgggatggggtggggtgggatgggatgggatgggatggggtggggtggggtggggt -gggatggggtgggatggggtgggatgggatggggtgggatgggatgggatggggtgggat -gggatggggtggggtggggtggggtgggatgaggtggggtgggatgggatgggatggggt -ggggtggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgggat -gcgatgggatgagatgagatggatggcatgggatgggtgggaggggatgggatattatca -gatggcaaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcat ->ref_chr20:48449684-48450495 -agtgcatcttgaacagtatttttaagctgggataagtggaataggaaggagtggagtgga -gcatgatggtatgggatgggatggatgggatgggatggatggatggatggggtgggatgg -gatgggatgggatgggatggatggatgggatggatggatgggatgggataggatggatgg -ggtgagatgggatggaatggatgggatgggatggatggatgggatgggatggatgggatg -ggatggatgggatgggatggatgggatggatgggatggaatgggatggatgggatgggat -gggattggatggggtgggatgggatggatggatgggatggatggatgggatggaatggat -ggatgggatgggatggatgggatgggatggatggatgggatgggatggatgcaatggatg -gatgggatgggatgggatgggatggatggaatggatggatgggatgggatgggatggatg -gggtgggatgagatggatgggatggatgggatgggatggatggatggatgggatgggatg -gatggatgggatgggatgggatggggt------------------------ggatgggat -ggatggatggatgggatgggatggatggatgggatgggatggatgggatgggatg----g -ggtggggtggggtgggatgggatgggatggggtggggtgggatgggattggatggggtgg -gatgcgatgggatgagatgagatggatggcatgggatgggtgggaggggatgggatatta -tcagatgg---------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------caaaagtaagaagtgttcatattttgtcttcaaaatataaatatgagtgcat diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f270e4c008a654fea706365c10826ee0.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f270e4c008a654fea706365c10826ee0.msa deleted file mode 100644 index fb68de54..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f270e4c008a654fea706365c10826ee0.msa +++ /dev/null @@ -1,175 +0,0 @@ ->syndip_1_chr20:63491847-63492500 -tgaatggatggatggggaggtggatggatagatggatggatggatggatggatggatgga -tggatggggggatagatggatggatggatggatggacggacggatggggagg-------- -tggatggatggatggatggatggatggatggatggatgaggagatgaacggatggatgag -atggatggatggatgatggagggaaggatggctgggtggggagatggatggatagagagg -tggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatggg -gaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtagggaga -tggatggatggatggatggggagggatggatggatggatggatggatgggtggatggata -gaaggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatggata -gatggata----gatggatggatggatggatggatggagagaaggatggatgggtgggga -ggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatg -gatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtgggga -ggtgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatggatg -gatggatgcatggatggatgga-------------------------------------- ------------------------------------------------------------- ------------------tggagaggtgggtggacggatggatggattgggaggtgggtag -atgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatgg -atggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggacag -aaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatgg -atagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgg -gtggggagatggatggatggatggatggatggatggatggatggacagaaggatgtatgg -gtgggtaggtgggtggatagatggatggatggatggatggataaatggatggatggaagg -atggatggataggtaggtgggtggatggatggatggatggatgtacagaaggatggatgg -gtgggtaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtgg -gtcaatagatggatggatagagagaaggatggatgggtggggagatggatggatggatgg -atggatggatggatggatggatggatagagagaaggatggatggttgagaca----atgg -atggatggatggatggagagatggatggatggacggatggacagaaggatggatgggtgg -ggaggtggatggatggattgaaggatggatgggtgggga----catggatggatggatgg -atggatggatggatggatggacagaaggatgt--------atgggtggggaggtgggtgg -atagatggatggatggggaaatggatggatggaaggatggatggatagggaggtgggtgg -atggatggatggatggatgtacagaaggatggatgggtggggaggtgggtgagtggatga -atggatggatggatagatagaaggatggatgggtgggacaatagatggatggatagagag -aaggatggatgggtggggagatagatggatggatggatggatggatggatagagagaagg -atggatggttgagacaatggatggatggatggatggatggagagatggatggatggatgg -atggacagaag ->syndip_2_chr20:63491847-63492500 -tgaatggatggatggggaggtggatggatagatggatggatggatggatggatggatgga -tggatggggggatagatggatggatggatggatggacggacggatggggaggtggatgga -tggatggatggatggatggatggatggatggatggatgaggagatgaacggatggatgag -atggatggatggatgatggagggaaggatggctgggtggggagatggatggatagagagg -tggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatggg -gaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtagggaga -tggatggatggatggatgcggagggatggatggatggatggatggatgggtggatggata -gaaggatggatgggtggggaggtgggtgggtgggtgcgtggatggatggagagatggata -gatggatagatggatggatggatggatggatggatggagagaaggatggatgggtgggga -ggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatg -gatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtgggga -ggtgggtgggtggatggatggatgagtggggaggtgggtgggtggatggatggatggatg -gatgcatggatggatggatggagaggtgggtggatgggtggatggacagaaggatggatg -ggtggggaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatggatg -gatgaaggatggatgggtggggaggtgggtggacggatggatggattgggaggtgggtag -atgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatgg -atggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggacag -aaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatgg -atagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgg -gtgggga----gatggatggatggatggatggatggatggatggacagaaggatgtatgg -gtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaagg -atggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggatgg -gtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtgg -gacaatagatggatggatagagagaaggatggatgggtgggga--------gatggatgg -atggatggatggatggatggatggatagagagaaggatggatggttgagacaatggatgg -atggatggatggatggagagatggatggatggatggatggacagaaggatggatgggtgg -ggaggtggatggatggattgaaggatggacgggtggggagatggatggatggatggatgg -atggatggatggatggatggacagaaggatgtatgggtgggtaggtgggtggatagatgg -atggatggatggatggataaatggatggatggaaggatggatggataggtaggtgggtgg -atggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatga -atggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagag -aaggatggatgggtggg----tagatggatggatggatggatggatggatagagagaagg -atggatggttgagacaatggatggatggatggatggatggagagatggatggatggatgg -atggacagaag ->p:HG002_1_chr20:63491847-63492500 -tgaatggatggatggggaggtggatggatagatggatggatggatggatggatggatgga -tggatggggggatagatggatggatggatggatggacggacggatggggaggtggatgga -tggatggatggatggatggatggatggatggatggatgaggagatgaacggatggatgag -atggatggatggatgatggagggaaggatggctgggtggggagatggatggatagagagg -tggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatggg -gaggtggatggatggataggtggatgggtggatggacagaaggatgaatgggtagggaga -tggatggatggatggatgcggagggatggatggatggatggatggatgggtggatggata -gaaggatggatgggtggggaggtgggtgggtgggtgcgtggatggatggagagatggata -gatggatagatggatggatggatggatggatggatggagagaaggatggatgggtgggga -ggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatg -gatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtgggga -ggtgggtgggtggatggatggatgagtggggaggtgggtgggtggatggatggatggatg -gatgcatggatggatggatggagaggtgggtggatgggtggatggacagaaggatggatg -ggtggggaggtgggtgagtgggtggatggatgaatggggaggtggatggatggatggatg -gatgaaggatggatgggtggggaggtgggtggacggatggatggattgggaggtgggtag -atgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatgg -atggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggacag -aaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatgg -atagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgg -gtgggga----gatggatggatggatggatggatggatggatggacagaaggatgtatgg -gtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaagg -atggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggatgg -gtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtgg -gacaatagatggatggatagagagaaggatggatgggtgggga--------gatggatgg -atggatggatggatggatggatggatagagagaaggatggatggttgagacaatggatgg -atggatggatggatggagagatggatggatggatggatggacagaaggatggatgggtgg -ggaggtggatggatggattgaaggatggacgggtggggagatggatggatggatggatgg -atggatggatggatggatggacagaaggatgtatgggtgggtaggtgggtggatagatgg -atggatggatggatggataaatggatggatggaaggatggatggataggtaggtgggtgg -atggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatga -atggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagag -aaggatggatgggtggg----tagatggatggatggatggatggatggatagagagaagg -atggatggttgagacaatggatggatggatggatggatggagagatggatggatggatgg -atggacagaag ->p:HG002_2_chr20:63491847-63492500 -tgaatggatggatggggaggtggatggatagatggatggatggatggatggatggatgga -tggatggggggatagatggatggatggatggatggacggacggatggggaggtggatgga -tggatggatggatggatggatggatggatggatggatgaggagatgaacggatggatgag -atggatggatggatgatggagggaaggatggctgggtggggagatggatggatagagagg -tggatgggtggatggggagatggatggatggatggatggatggggaagtggatggatggg -gaggtggatggatggatgtatgggtgggtggatggacagaaggatgaatgggtagggaga -tggatggatggatggatggggagggatggatggatggatggatggatgggtggatggata -gaaggatggatgggtggggaggtgggtgggtgg----gtggatggatggagagatggata -gatggata----gatggatggatggatggatggatggagagaaggatggatgggtgggga -ggtgggtgggtgggtggatgggtggatggatggatgggtggggaggtgggcgggtggatg -gatggatggatgcagaggtgggtggatggatggatggagagaaggatggatgggtgggga -ggtgggtgggtggatggatggatgagtggggaggtgggtgggtgggtggatggatggatg -gatggatgcatggatggatgga-------------------------------------- ------------------------------------------------------------- ------------------tggagaggtgggtggacggatggatggattgggaggtgggtag -atgggtggatggacagaaggatggatgggtggggaggtgggtgggtgggtggatggatgg -atggggaggtggatggatggatggttagatggggaggtgggtggatgggtggatggacag -aaggatggatgggtagggaggtaggtgagtggatggatggatggggagatggatggatgg -atagagagaaggatggatgggtgggacaatggatggatggatggatagaaggatggacgg -gtggggagatggatggatggatggatggatggatggatggatggacagaaggatgtatgg -gtggggaggtgggtggatagatggatggatggatggatggggaaatggatggatggaagg -atggatggatagggaggtgggtggatggatggatggatggatgtacagaaggatggatgg -gtggggaggtgggtgagtggatgaatggatggatggatagatagaaggatggatgggtgg -gacaatagatggatggatagagagaaggatggatgggtggggagatggatggatggatgg -atggatggatggatggatggatggatagagagaaggatggatggttgagaca----atgg -atggatggatggatggagagatggatggatggacggatggacagaaggatggatgggtgg -ggaggtggatggatggattgaaggatggatgggtgggga----catggatggatggatgg -atggatggatggatggatggacagaaggatgt--------ataggtgggtggatagatgg -atggatggatggatggataaatggatggatggaaggatggatggataggtaggtgggtgg -atggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatga -atggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagag -aaggatggatgggtggg----tagatggatggatggatggatggatggatagagagaagg -atggatggttgagacaatggatggatggatggatggatggagagatggatggatggatgg -atggacagaag ->ref_chr20:63491847-63492500 -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------------------------gaatggatgg -atggggaggtggatggatagatggatggatggatggatggatggatggatggatgggggg -atagatggatggatggatggatggacggacggatggggaggtggatggatggatggatgg -atggatggatggatggatggatggatgaggagatgaacggatggatgagatg----gatg -gatggatgatggagggaaggatggctgggtggggagatggatggatagagaggtggatgg -gtggatggggagatggatggatggatggatggatgggga----agtggatggatggggag -gtggatggatggatgtatgggtgg----------------gtaggtgggtggatagatgg -atggatggatggatggataaatggatggatggaaggatggatggataggtaggtgggtgg -atggatggatggatggatgtacagaaggatggatgggtgggtaggtgggtgagtggatga -atggatggatggatagatagaaggatggatgggtgggtcaatagatggatggatagagag -aaggatggatgggtggg----tagatggatggatggatggatggatggatagagagaagg -atggatggttgagacaatggatggatggatggatggatggagagatggatggatggatgg -atggacagaag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f3831c7aa56873b3e61fa9717d076cc2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f3831c7aa56873b3e61fa9717d076cc2.msa deleted file mode 100644 index c15dd175..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f3831c7aa56873b3e61fa9717d076cc2.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:61100811-61102515 -ctgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacat -cctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgt -gtcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtca -cacctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacc -tggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccgga -gagaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagaga -ccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagacccc -gagtgagggcagatggccacatcctctacttcctgtgtcacacctggggagaccctgagt -gagggcaga--------------------------------------------------- ------cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcag -acagccacctcctctacttcctgtgtcacacct--------------------------- ------------------------------ggagagactccaagtgaggagagacggccac -atcttctacttcctgtgtcacacctggagagacctcgagtgagggcagatggccacatcc -tctaattcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctcta -cttcctgtgtcacacctggagagaccccaagtgagggcagactgccacctcctctacttc -ctgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgt -gccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtca -cacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacc -tggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagaga -ccccgagtgagggcatatggccacatcctctaattcctatgtcacacctggagagacccc -gagtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagt -gagggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagg -gcagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcag -acagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacag -ctaccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccac -ctcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcc -tctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctcta -tttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattc -ctgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgt -gtcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtca -cacctggggagacc ->syndip_2_chr20:61100811-61102515 -ctgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacat -cctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgt -gtcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtca -cacctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacc -tggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccgga -gagaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagaga -ctccaagtgaggagagacggccacatcttctacttcctgtgtcacacctggagagacctc -gagtgagggcagatggccacatcctctaattcctgtgtcacacctggagagaccccaagt -gagggcagactgccacctcctctacttcctgtgtcacacctagagagaccccgagtgagg -acagccagccatgtcctctacttcctgtgccacatccggagagatcccgagtgagggcag -acagccatgtcctctacttcctgtgtcacacctggagagaccccgagtgagggcagacgg -ccacatcctctaattcctgtgtcacacctggagagaccccgagtgagggcagacggccac -atcctctaattcctgtgtcatgcctggagagaccccgagtgagggcatatggccacatcc -tctaattcctatgtcacacctggagagaccccgagtgagggtggatggccacatcctcta -attcctgtgtcatacctggagagaccccgagtgagggcagatggccacctcctctacttc -ctgtgtcacacctggagagaccccaagtgagggcagacagccatgtcctctacgtcctgt -gccacatccggagagaccccga-tgagggcagacagctaccccctctacttcctgtgtca -cacctgcagagaccccaagtgagggcagatggccacctcttctacttcctgtgtcacacc -tggagaggccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctatttcctgtgtcacacctggagaga -ccccgagtgagggcagacggccacatcctctaattcctgtgtcacacatggagagacccc -gagtgaaggcagaaggccacatcctctacttcctgtgtcacacctagagagaccccgagt -gagggcggatggccacatcctctaattcctatgtcacacctggagagaccccgagtgagg -gtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagtgagggcag -atggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcagacag -ccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacagctac -cccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccacctct -tctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcctcta -cttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattc -ctgtgtcacacatggagagaccctgagtgagggcagaaggccacatcctctacttcctgt -gtcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtca -cacctggggagacc ->p:HG002_1_chr20:61100811-61102515 -ctgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacat -cctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgt -gtcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtca -cacctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacc -tggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccgga -gagaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagaga -ccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagacccc -gagtgagggcagatggccacatcctctaattcctgtgtcacacctggagaaaccccaagt -gagggcagactgccacctcctctacttcctgtgtcacacctagagagaccccgagtgagg -acagccagccatgtcctctacttcctgtgccacatccggagagatcccgagtgagggcag -acagccatgtcctctacttcctgtgtcacacctggggagaccctgagtgagggcagacag -ccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcagacagccac -ctcctctacttcctgtgtcacacctggagagactccaagtgaggagagacggccacatct -tctacttcctgtgtcacacctggagagacctcgagtgagggcagatggccacatcctcta -attcctgtgtcacacctggagagaccccaagtgagggcagactgccacctcctctacttc -ctgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgt -gccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtca -cacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacc -tggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagaga -ccccgagtgagggcatatggccacatcctctaattcctatgtcacacctggagagacccc -gagtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagt -gagggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagg -gcagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcag -acagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacag -ctaccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccac -ctcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcc -tctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctcta -tttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattc -ctgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgt -gtcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtca -cacctggggagacc ->p:HG002_2_chr20:61100811-61102515 -ctgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacat -cctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgt -gtcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtca -cacctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacc -tggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccgga -gagaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagaga -ccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagacccc -gagtgagggcagatggccacatcctctacttcctgtgtcacacctggggagaccctgagt -gagggcaga--------------------------------------------------- ------cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcag -acagccacctcctctacttcctgtgtcacacct--------------------------- ------------------------------ggagagactccaagtgaggagagacggccac -atcttctacttcctgtgtcacacctggagagaccccgagtgagggtggatggccacatcc -tctaattcctgtgtcatacctggagagacctcgagtgagggcagatggccacatcctcta -attcctgtgtcacacctggagagaccccaagtgagggcagactgccacctcctctacttc -ctgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgt -gccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtca -cacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacc -tggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagaga -ccccgagtgagggcatatggccacatcctctaattcctatgtcacacctggagagacccc -gagtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagt -gagggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagg -gcagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcag -acagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacag -ctaccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccac -ctcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcc -tctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctcta -tttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattc -ctgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgt -gtcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtca -cacctggggagacc ->ref_chr20:61100811-61102515 -ctgacaagtcctgtgactggagagaccccgagtgaaggcagacctccatgtcctctacat -cctgtgccacatctggagagacccctgtgagggcagagagctacctcctcttcttcctgt -gtcacacctggagagaccccgagtgagggcggatggccacgtcttctacttcctgtgtca -cacctggagagaccccgagtgagggcagatggccacatcctctacttcctgtgtcacacc -tggggagaccctgagtgagggcagacagccatgtcctctacgtcctgtgccacatccgga -gagaccccaagagagggcagacagccacctcctctacttcctgtgtcacacctggagaga -ccccgagtgagggcggatggccacgtcttctacttcctgtgtcacacctggagagacccc -gagtgagggcagatggccacatcctctacttcctgtgtcacacctggggagaccctgagt -gagggcaga--------------------------------------------------- ------cagccatgtcctctacgtcctgtgccacatccggagagaccccaagagagggcag -acagccacctcctctacttcctgtgtcacacct--------------------------- ------------------------------ggagagactccaagtgaggagagacggccac -atcttctacttcctgtgtcac--------------------------------------- ------------------acctggagagacctcgagtgagggcagatggccacatcctcta -attcctgtgtcacacctggagagaccccaagtgagggcagactgccacctcctctacttc -ctgtgtcacacctagagagaccccgagtgaggacagccagccatgtcctctacttcctgt -gccacatccggagagatcccgagtgagggcagacagccatgtcctctacttcctgtgtca -cacctggagagaccccgagtgagggcagacggccacatcctctaattcctgtgtcacacc -tggagagaccccgagtgagggcagacggccacctcctctacttcctgtgtcacacctgga -gagaccccgagtgagggcagacggccacatcctctaattcctgtgtcatgcctggagaga -ccccgagtgagggcatatggccacatcctctaattcctatgtcacacctggagagacccc -gagtgagggtggatggccacatcctctaattcctgtgtcatacctggagagaccccgagt -gagggcagatggccacctcctctacttcctgtgtcacacctggagagaccccgagtgagg -gcagatggccacctcctctacttcctgtgtcacacctggagagaccccaagtgagggcag -acagccatgtcctctacgtcctgtgccacatccggagagaccccga-tgagggcagacag -ctaccccctctacttcctgtgtcacacctgcagagaccccaagtgagggcagatggccac -ctcttctacttcctgtgtcacacctggagaggccccgagtgagggcagacggccacctcc -tctacttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctcta -tttcctgtgtcacacctggagagaccccgagtgagggcagacggccacatcctctaattc -ctgtgtcacacatggagagaccccgagtgagggcagaaggccacatcctctacttcctgt -gtcacacctagagagaccccgagtgagggcggatggccacatcctctaattcctgtgtca -cacctggggagacc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f421dd5eadc752e68b598f461ab861a8.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f421dd5eadc752e68b598f461ab861a8.msa deleted file mode 100644 index faa3b7a3..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f421dd5eadc752e68b598f461ab861a8.msa +++ /dev/null @@ -1,85 +0,0 @@ ->syndip_1_chr20:23155404-23156075 -gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct -gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc -ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg -gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga -gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa -agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa -ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga -gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga -aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag -agaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag -agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag -gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag -gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg -gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccc ->syndip_2_chr20:23155404-23156075 -gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct -gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc -ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg -gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga -gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa -agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa -ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga -gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga -aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag -----agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag -agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag -gaaagaaag------------------------aagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag -gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg -gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccc ->p:HG002_1_chr20:23155404-23156075 -gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct -gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc -ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg -gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga -gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa -agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa -ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga -gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga -aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag -----agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag -agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag -gaaagaaag------------------------aagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag -gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg -gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccc ->p:HG002_2_chr20:23155404-23156075 -gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct -gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc -ctgcagcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggg -gaggggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgagggga -gggggggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaa -agaagaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaa -ggaaaggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaaga -gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga -aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag -agaaagaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag -agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag -gaaagaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag -gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg -gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccc ->ref_chr20:23155404-23156075 -gggaaagacacagaggtagaatctgcgttaggaataaaaaccgctactctccgttgttct -gtgtgcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgcc -ctgcagcacaaaagaggaaggaaagcaag-------------------ggaagggaaggg -gaggggaggaaggga--------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------aggaaaagagagagaaagagaaaga -gagaaagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaagga -aggaagaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag ---------agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaag -agaaaagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaag -gaaagaaag------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaag -gtcttaacaccttggtaatttttgtgctcttccctggactttggactttgcagccttagg -gagacagagctctttaatgtacactttcccatcaggcactgcatggccaagaacctgcct -gcaaagccccc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f4e3f62513b4265dafe6aa31b6f67cd4.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f4e3f62513b4265dafe6aa31b6f67cd4.msa deleted file mode 100644 index fc989fd9..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f4e3f62513b4265dafe6aa31b6f67cd4.msa +++ /dev/null @@ -1,475 +0,0 @@ ->syndip_1_chr20:20354469-20358424 -ctccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaaatcaggta -cagaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcat -aagggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgag -ggaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcaca -ctgtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggagg -tggtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgaga -gaaaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactg -tgtcagaggaggtggtcacactgaggggaggtggtcacactgtgagaggggaggtggtca -gactctgtcagaggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagt -ggtcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagaggg -gaggtgatcacactgagggg-----------------------aggtggtcacactgtga -gagggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtc -acactgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggaga -aggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggt -ggtcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggt -cacactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtgg -tcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtg -gtcacactgaggggaggtactcacactgtgaggggaggtggtcacactgtgaggggaggt -ggtcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggagg -gggtcacactgtgagggggaaggtggtcacactgtgagaggggagaaggtcacactaagg -ggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgag -aggaggtggtcacactgtgaggggaggtcacactgaggggaggtagtgacactatgagca -gagatggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagc -agagatggtcacactgtgaggggaggtggtcacactgaggggaggtagtcacactgtgag -gggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtga -gcagagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacac -tgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatca -cactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcaca -ctgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcac -actgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtca -cactgaggggaggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtc 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-ctccagtctgggtgacagagagagaccttgtctc--aaaaaaaaaaaaaaaaatcaggta -cagaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcat -aagggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgag -ggaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcaca -ctgtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggagg -tggtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgaga -gaaaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactg -tgtcagaggaggtggtcacactgaggggaggtggtcacactgtgagaggggaggtggtca -gactctgtcagaggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagt -ggtcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagaggg -gaggtgatcacactgaggggaggtggtcacactgtgagagggaaggtggtcacactgtga -gagggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtc -acactgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggaga -aggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggt -ggtcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggt -cacactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtgg -tcacactgaggggaggtagtgacactgtgagcagaga----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------tggtcacactgtgaggggaggtggtcacactgaggggaggtactcacactgtgag -gggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtga -gcagagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacac -tgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatca -cactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcaca -ctgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcac -actgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtca -cactgaggggaggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtc -acactgaggggaggtagtgacactgtgagcagagatggtcacactgtaaggggaggtgat 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-tgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcaca -ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactg -aggggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagt -gtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacac -tgaggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcaca -ctgagaggaggtggtcacactgaggggaggtggtcacactgaggggaagtggtcacactg -aggggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgag -gggaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatg -agaggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatattt -gcctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga ->p:HG002_1_chr20:20354469-20358424 -ctccagtctgggtgacagagagagaccttgtctc--aaaaaaaaaaaaaaaaatcaggta 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------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------tggtcacactgtgaggggaggtggtcacactgaggggaggtactcacactgtgag -gggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtga -gcagagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacac -tgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatca -cactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcaca -ctgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcac -actgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtca -cactgaggggaggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtc -acactgaggggaggtagtgacactgtgagcagagatggtcacactgtaaggggaggtgat -cacactgtgaggggacgtggtcacactgtgaggggaggtggtcacactgtgagaggggag 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-ggggaggtggtcacac------tggggaggtggtcacactgtgaggggaggtggtcacac -tgtgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtcaca -ctgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcac -actgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatact -gtgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcac -actgtgaagggtggtagtcacactgagaggaggtggtcaca--ctgaggggaagtggtca -cactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcat -agtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcatag -tgtgaggggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaagtagtcacactgaggggaagtggtcacac -tgaggggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcaca -ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatact -gtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcacac -tgtgaggggaggtggtcacactgagaggaggtggtcacactgaggggaggtggtcatact -gtgagtgaggaggtagtcacactgaggggaagtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggagggggtcata -ctgcgagtggaggtagtcacactgtgaagggtggtagtcaca--ctgagaggaggtggtc -acactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtca -cactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcat -agtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtca -tactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcac -agtgtgcggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtca -tactgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcac -actgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -actgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtgacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcaca -ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactg -aggggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagt -gtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacac -tgaggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcaca -ctgagaggaggtggtcacactgaggggaggtggtcacactgaggggaagtggtcacactg -aggggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgag -gggaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatg -agaggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatattt -gcctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga ->p:HG002_2_chr20:20354469-20358424 -ctccagtctgggtgacagagagagaccttgtctcaaaaaaaaaaaaaaaaaaatcaggta -cagaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcat -aagggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatggtcacactgag -ggaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcaca -ctgtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggagg -tggtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgaga -gaaaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactg -tgtcagaggaggtggtcacactgaggggaggtggtcacactgtgagaggggaggtggtca -gactctgtcagaggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagt -ggtcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagaggg -gaggtgatcacactgagggg-----------------------aggtggtcacactgtga -gagggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtc -acactgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggaga -aggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggt -ggtcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggt -cacactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtgg -tcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtg -gtcacactgaggggaggtactcacactgtgaggggaggtggtcacactgtgaggggaggt -ggtcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggagg -gggtcacactgtgagggggaaggtggtcacactgtgagaggggagaaggtcacactaagg -ggaggtagtcacactgtgaggggaggtgatcacactaaggggaggtggtcacactgtgag -aggaggtggtcacactgtgaggggaggtcacactgaggggaggtagtgacactatgagca -gagatggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtgagc -agagatggtcacactgtgaggggaggtggtcacactgaggggaggtagtcacactgtgag -gggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtga -gcagagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacac -tgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatca -cactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcaca -ctgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcac -actgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtca -cactgaggggaggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtc -acactgaggggaggtagtgacactgtgagcagagatggtcacactgtaaggggaggtgat -cacactgtgaggggacgtggtcacactgtgaggggaggtggtcacactgtgagaggggag -gtgaccacacaggggaggtggtcacactgaggggaggtagtgacactgtgagcagaggtg -gtcacactgtgaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggt -ggtcacactgaggggaagtggtcacactgagggggggtggtcacactgaggggaggtggt -catactgtgagtgaggaggtagtcacactgaggggaggggtcatactgcgagtggaggtg -gtcacactgtgaagggtggtagtcacactgagaggaggtgttcacactgaggggaagtgg -tcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggt -catagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtc -acagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggt -cacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtc -atagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtca -cactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcaca- --ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtca -cactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactggggaggtggtcacactgt -gaggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactg -aggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtgtga -ggggaggtggtcatactgtgagtgaggaggtagtcacac--tgaggggagggggtcatac -tgcgagtggaggtagtcacactgtgaagggtggtagtcacactgagaggaggtggtcaca -ctgaggggaagtggtcacactgaggggaggtggtcatactg------------------- ----------------------tgaggggaagtggtcacactgaggggaggtggtcatagt -gtga--ggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -ac--tgaggggaggtggtcacactgaggggaggtggtcacagtgtgagaggaggtggtca -cactgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcac -agtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtcac -actgaggggaggtggtcacagtgtgaggggagatggtcacactgaggggaggtggtcaca -gtgtgaggggaggtggtcacactgaggggaggtggtcaca-------------------g -tgtgaggggaggtggtcacactgaggggaggtggtcacactgagaggaggtggtcacact -gaggggaggtggtcatactgtgagtgaggaggtagtcacactgaggggaagtggtcacac -tgaggggaggtg------------------------------------------gtcaca -ctgaggggagggggtcatactgcgagtggaggtagtcacactgtgaagggtggtagtcac -actgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatact -gtgaggggaagtggtcacactgaggggaggtggtcatagtgtgaggggag---------- ------------------------------------------------------------- --------------------------------gtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcacagtgtga--ggggaggtggtcacactgaggggaggtggtcaca -gtgtacggggaggtggtcatac--tgaggggaggtggtcacagtgtgaggggaggtggtc -acactgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgtgaggggaggtggtcacactgaggagaggtggtcat -agtgtgaggggaggtggtcacactgaggggaggtggtcaca-c-tgaggagaggtggtca -t-------------------agtgtgaggggaggtggtcacac----------------- ------------------------------------------------------------- -------------------------tgaggggaggtggtcacactgaggggaggtggtcat -agtgtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtca -cactgaggggaggtggtcacactgaggggaggtggtcatagtgtgaggggaggtggtcac -agtg--------------------------------------tgaggggaggtggtcaca -ctgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgtgaggggaggtggtcaca -ttgaggagaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggagaggtggtcatagt -gtgcggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacagtg -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactg -aggggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagt -gtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacac -tgaggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcaca -ctgagaggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtcacactg -aggggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgag -gggaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatg -agaggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatattt -gcctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga ->ref_chr20:20354469-20358424 -ctccagtctgggtgacagagagagaccttgtctc-aaaaaaaaaaaaaaaaaatcaggta -cagaaaggtaaatactgcacgatctcacttacatgtggaatctaaagaagttgaattcat -aagggtaatgaggggaggaaggggtggtcatactgtgtgaagggagatagtcacactgag -ggaaggtggtcacactgtgagaagggaggtagtcacattgtgagagaaaaagtgatcaca -ctgtgtgaggggaggtggtcacactgtgagagaaaaagtaatcatactgtgaaagggagg -tggtcacgctgagaggggaggtggtcacactgtgtcaggggaggtggtcacactgtgaga -gaaaaagtaatcacactgtgaggggatgtggtcacactgagaggggaggtggtcagactg -tgtcagaggaggtggtcacactgagg---------------------------------- -------------ggaggtggtcacactgtgagaggggaggtggtcacactgaggggaagt -ggtcacactgtgagaggggaggtggtcacactgaggggagatggtcacactgcaagaggg -gaggtgatcacactgagggg-----------------------aggtggtcacactgtga -gagggaaggtggtcacactgtgagagggaaggtggtcacactgtgtgaggggaggtggtc -acactgtgaggggaggtggtcacattgtgagagggaagggggtcactgtgagaggggaga -aggtcacactaaggggaggtagtcacactgtgaggggaggtgatcacactaaggggaggt -ggtcacactgtgagaggaggtggtcacactgtgaggggtggtcacactgtgaggggaggt -cacactgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtgg -tcacactgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtg -gtcacactgaggggagg------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------tggtcacactgtgaggggaggtggtcacactgaggggaggtggtcacactgtgag -gggaggtggtcacactgtgaggggaggtggtcacactgaggggaggtagtgacactgtga -gcagagatggtcacactgtgaggggagggggtcacactgtgagggggaaggtggtcacac -tgtgagaggggagaaggtcacactaaggggaggtagtcacactgtgaggggaggtgatca -cactaaggggaggtggtcacactgtgagaggaggtggtcacactgtgaggggaggtcaca -ctgaggggaggtagtgacactatgagcagagatggtcacactgtgaggggaggtggtcac -actgaggggaggtagtgacactgtgagcagagatggtcacactgtgaggggaggtggtca -cactgaggggaggtagtcacactgtgaggggaggtggtcacactgtgaggggaggtggtc -acactgaggggaggtagtgacactgtgagcagagatggtcacactgtaaggggaggtgat -cacactgtgaggggac---gtcacactgtgaggggaggtggtcacactgtgagaggggag -gtgaccacacaggggaggtggtcacactgaggggaggtagtgacactgtgagcagagatg -gtcacactgtgaggggaggtggtcacac--tgaggggaggtagtcacactgagaggaggt -ggtcacactgaggggaagtggtcacactgagggggggtggtcacactgaggggaggtggt -catactgtgagtgaggagctagtcacactgaggggaggggtcatactgcgagtggaggta -gtcacactgtgaagggtggtagtcacactgagaggaggtggtcacactgaggggaagtgg -tcacactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggt -catagtgtgaggggaggtggtcacactgaggggaggtggtcacactgaggggaggtggtc -acagtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggagatggt -cacactgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtc -atagtgtgaggggaggtggtcacactggggaggtggtcacactgtgaggggaggtggtca -cactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcatag -tgtgaggggaggtggtcacact----ggggaggtggtcacactgtgaggggaggtggtca -cactgagaggaggtggtcacactgaggggaagtggtcacactgaggggaggtggtcacac -tgaggggaggtggtcatagtgtgaggggaggtggtcacact------------------- ---ggggaggtggtcacactgtgaggggaggtggtcacactgagaggaggtggtcacactg -aggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatagtgtga -ggggaggtggtcacac------tggggaggtggtcacactgtgaggggaggtggtcacac -tgtgaggggaggtggtcacac--tgagaggaggtggtcacactgaggggaagtggtcaca -ctgagaggaggtggtcacactgaggggaggtggtcatactgtgagtgaggaggtagtcac -actgaggggaagtggtcacactgaggggaggtggtcacactgaggggaggtggtcatact -gtgagtgaggaggtagtcacactgaggggagggggtcatactgcgagtggaggtagtcac -actgtgaagggtggtagtcacactgagaggaggtggtcaca--ctgaggggaagtggtca -cactgaggggaggtggtcatactgtgaggggaagtggtcacactgaggggaggtggtcat -agtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgaggggaggtggtca -cactgaggggaggtggtcaca--------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------g -tgtgcggggaggtggtcatactgaggggaggtggtcacactgaggggaggtggtcacact -gaggggaggtggtcatactgtgagt----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------gaggaggtagtcacactgaggggagggggtcata -ctgcgagtggaggtagtcacactgtgaagggtggtagtcaca--ctgagaggaggtggtc -acactgaggggaagtggtcacactgaggggaggtggtcatactgtgaggggaagtggtca -cactgaggggaggtggtcatagtgtgaggggaggtggtcacactgaggggaggtggtcac -agtgtgaggggaggtggtcacactgaggggaggtggtcacagtgtgcggggaggtggtca -t----------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------actgaggggaggtggtcacagtg -tgaggggaggtggtcacagtgtgaggggaggtggtcacactgaggggaggtggtcatagt -gtgaggggaggtggtcacactgaggggaggtggtcacactgagggaaggtggtcacactg -aggggaggtggtcatagtgtgaggggaggtggtcatagtgtgaggggaggtggtcacagt -gtgaggggaggtggtcacactgaggagaggtggtcatagtgtgaggggaggtggtcacac -tgaggggaggtggtcacactgtgaggggaggtgggcacactgtgaggggtggtagtcaca -ctgagaggaggtggtcacactgaggggaggtggtcacactgaggggaagtggtcacactg -aggggaatggtcatactgtgaggggaggtggtcacactgaggggaagtggtcacactgag -gggaatggtcatactgtgaggggaggtggtcacactgtgaaagaagatgatcacagtatg -agaggtcatccttcaagaggcaagtgcccaaaaatctgtttataatctagagcaatattt -gcctgaaataaactttaaaagtggttttacgctatttaacccagtgtcaga diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f59aef8f67e99a822944ec0132cdd81b.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f59aef8f67e99a822944ec0132cdd81b.msa deleted file mode 100644 index 4be9d41e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f59aef8f67e99a822944ec0132cdd81b.msa +++ /dev/null @@ -1,140 +0,0 @@ ->syndip_1_chr20:53203886-53204574 -acataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactg -taagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatct -ccttcatttttataatatgatactattatatcataattttataatatactattatatcat -attatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatga -tatactattatatcatcatatgatgatatgatactatatcatcatatgatgatatgatac -tatatcatcatatgatgat---atactatatcatcatatgatgatatgatactatatcat -catatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgat -gatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgat -actatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatc -atcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatg -atgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatg -atactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactata -tcatcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcaca -tgatgatatgatactatatcatcacatgatgatatg--atactatatcatcacatgatga -tatgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatac -tatatcatc--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------acatgatgatatgatacta -tatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatac -tatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgat -actatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatg -atactattatatcataatatgatataatattttggacatactaggttaaataagatatag -ttatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatat -gaaattccatgcatagctgacattctacttctattg ->syndip_2_chr20:53203886-53204574 -acataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactg -taagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatct -ccttcatttttataatatgatactattatatcataattttataatatactattatatcat -attatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatga -tatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatac -tatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcat -catatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgat -gatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgat -actatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatc -atcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatg -atgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatg -atactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactata -tcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcata -tgatgatatgatactatatcatcatatgatgatatg--atactatatcatcatatgatga -tatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatac -tatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcat -catatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgat -gatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgat -actatatcataacatgatgatatgatactatatcataacatgatgatatgatactatatc -atcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactata -tcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatacta -tatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatac -tatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgat -actatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatg -atactattatatcataatatgatataatattttggacatactaggttaaataagatatag -ttatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatat -gaaattccatgcatagctgacattctacttctattg ->p:HG002_1_chr20:53203886-53204574 -acataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactg -taagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatct -ccttcatttttataatatgatactattatatcataattttataatatactattatatcat -attatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatga -tatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatac -tatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcat -catatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgat -gatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgat -actatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatc -atcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatg -atgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatg -atactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactata -tcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcata -tgatgatatgatactatatcatcatatgatgatatg--atactatatcatcatatgatga -tatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatac -tatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatcat -catatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgat -gatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgat -actatatcataacatgatgatatgatactatatcataacatgatgatatgatactatatc -atcatataacatgatgatatgatactatatcatcatataacatgatgatatgatactata -tcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatacta -tatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatac -tatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgat -actatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatg -atactattatatcataatatgatataatattttggacatactaggttaaataagatatag -ttatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatat -gaaattccatgcatagctgacattctacttctattg ->p:HG002_2_chr20:53203886-53204574 -acataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactg -taagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatct -ccttcatttttataatatgatactattatatcataattttataatatactattatatcat -attatatgatactatttatatcatcatatgatgatatactattatatcatcatatgatga -tatactattatatcatcatatgatgatatgatactatatcatcatatgatgatatgatac -tatatcatcatatgatgat---atactatatcatcatatgatgatatgatactatatcat -catatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatgat -gatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgat -actatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactatatc -atcatatgatgatatgatactatatcatcatatgatgatatgatactatatcatcatatg -atgatatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatg -atactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatactata -tcatcacatgatgatatgatactatatcatcacatgatgatatgatactatatcatcaca -tgatgatatgatactatatcatcacatgatgatatg--atactatatcatcacatgatga -tatgatactatatcatcacatgatgatatgatactatatcatcacatgatgatatgatac -tatatcatc--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------acatgatgatatgatacta -tatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgatac -tatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgat -actatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatg -atactattatatcataatatgatataatattttggacatactaggttaaataagatatag -ttatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatat -gaaattccatgcatagctgacattctacttctattg ->ref_chr20:53203886-53204574 -acataccacatggggctactaagcccttcaaatgtgactggtccaaattaaaatatactg -taagtataaaacacactgaacttgaaaggcttagtccaaaaaccgtagtgcacaatatct -ccttcatttttataatatgatactattatatcataattttataatatactattatatcat -attatatgatactatttatatcatcatatgatgatatgat-------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------atactatatcatcatatgatgatatgatatactatatcatcatatgatga -tatgatactatatcatcatatgatgatatgatactatatcatcatatgatgatatgatac -tatatcatc--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------atatgatgatatgatacta -tatcatcat-----atgatgatatgatactatatcatcatataacatgatgatatgatac -tatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatgat -actatatcatcatataacatgatgatatgatactatatcatcatataacatgatgatatg -atactattatatcataatatgatataatattttggacatactaggttaaataagatatag -ttatataaatcaatttcacttatttctttctcattctttaatgtgactactgaagcatat -gaaattccatgcatagctgacattctacttctattg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f5ab8103fdc862862724ddfcfe43644a.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f5ab8103fdc862862724ddfcfe43644a.msa deleted file mode 100644 index 39e41974..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f5ab8103fdc862862724ddfcfe43644a.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:61201583-61202574 -aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata -ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtta -gagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggacc -ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac -tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc -catcctcactcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg-g -tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc -ccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc--- --ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcac -ctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca------ -----------------------ccaggaccctccatgagtgtcacctccatcctcactca -ggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat -cctcactcaggaccctccat-ggtgtcaccgccatcctca-------------------- ------------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagga -tcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcct -cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcac -ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctccat -gagtgtcacctccatcctca--------------------------ctcaggaccctcca -tg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag -gaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat -cctcactcaggaccctccatg-gtgtcacctccatcctcaccaggaccctccatgagtgt -cacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccct -ccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc -aggaccctccatg-----------------------------------gtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcaccaggaccctccatgagtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc -cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct -caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt -cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggc ->syndip_2_chr20:61201583-61202574 -aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata -ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta -gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc -ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac -tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgggtgtcacctc -catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag -tgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggac -cctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctc -actcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcac -ctccatcctcactcaggaccctccatgggtgccacctccatcctcaccaggatcccctgt -aagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccc -tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactca -ggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccat -cctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtg -tcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcct -tactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccac -ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctccat -gagtgtcacctccatcctcaggaccctccatggtgtcacctccatcctcaggaccctcca -tgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag -gaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat -cctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggacact -ccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactc -aggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc -cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct -aaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt -cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggc ->p:HG002_1_chr20:61201583-61202574 -aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata -ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta -gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc -ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac -tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgggtgtcacctc -catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag -tgtcacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggac -cctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccatcctc -actcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcac -ctccatcctcactcaggaccctccatgggtgccacctccatcctcaccaggatcccctgt -aagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcctcaggaccc -tccatgagtgtcacctccatcctcaggaccctccatgagtgtcacctccatcctcactca -ggaccctccatggtgtcacctccatcctcactcaggaccctccat-ggtgtcacctccat -cctcactcaggaccctccatgggtgtcacctccatcctcactcaggaccctccatgagtg -tcacctccatcctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcagg -accctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatcct -tactcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccac -ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcactcaggaccctccat -gagtgtcacctccatcctcaggaccctccatggtgtcacctccatcctcaggaccctcca -tgagtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag -gaccctccatgggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat -cctcactcaggaccctccatgagtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctcactcaggaccctccatg-gtgtcacctccatcctcactcaggacact -ccatggtgtcacctccatccttactcaggaccctccatggtgtcaccgccatcctcactc -aggaccctccatgagtgccacctccatcctcaccaggatcccctgtaagtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc -cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct -aaggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt -cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggc ->p:HG002_2_chr20:61201583-61202574 -aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata -ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccgtta -gagaaggaatttcctcactcaggaccctctgcggatgtcacctccatcctcatcaggacc -ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac -tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc -catcctcactcaggatcccctgtaagtgtcacctccatcctcaccaggaccctccatg-g -tgtcaccgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatc -ccctgtaagtgtcacctccatcctcac-caggaccctccatgagtgtcacctccatc--- --ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctccat-ggtgtcac -ctccatcctcactcaggaccctccat-ggtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctca------ -----------------------ccaggaccctccatgagtgtcacctccatcctcactca -ggaccctccatggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat -cctcactcaggaccctccat-ggtgtcaccgccatcctca-------------------- ------------ctcaggaccctccatgagtgtcacctccatcctcactcaggaccctcca -tggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcaccagga -tcccctgtaagtgtcacctccatcctcaccaggaccctccatgagtgtcacctccatcct -cactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatg-gtgtcac -ctccatcctcaccaggatcccctgtaagtgtcacctccatcctcac-caggaccctccat -gagtgtcacctccatcctca--------------------------ctcaggaccctcca -tg-gtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcag -gaccctccat-ggtgtcacctccatcctcactcaggaccctccatgggtgtcacctccat -cctcactcaggaccctccatg-gtgtcacctccatcctcaccaggaccctccatgagtgt -cacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccct -ccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc -aggaccctccatg-----------------------------------gtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcaccaggaccctccatgagtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc -cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct -caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt -cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggc ->ref_chr20:61201583-61202574 -aatacagcatatcaaaatgtatgggatgcagctaaagcagtgctcagaggacaatctata -ctactagaggcttatattagaaaaaaaaatttaaatcaataacctaagctttcaccatta -gagaaggaatttcctcactcaggaccctctgcggatgtcgcctccatcctcatcaggacc -ctccatggtgtcacctccatcctcactcaggacactccatggtgtcacctccatccttac -tcaggaccctccatggtgtcaccgccatcctcactcaggaccctccatgagtgccacctc -catcctcac-caggatcccctgtaagtgtcacctccatcctcaccaggaccctccatgag -tgtcacctccatcct--------------------------------------------- -----------------------------caggaccctccatgagtgtcacctccatcctc -actcaggaccctccat------------------------------------ggtgtcac -cgccatcctcactcaggaccctccatgagtgccacctccatcctcaccaggatcccctgt -aa---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------gtgtcacctccatcctcaccaggaccctccatgagtgt -cacctccatc----ctcaggaccctccatgagtgtcacctccatcctcactcaggaccct -ccatggtgtcacctccatcctcactcaggaccctccatggtgtcacctccatcctcactc -aggaccctccatg----------------------------------ggtgtcacctcca -tcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctccatggtgt -cacctccatcctcactcaggaccctccatggtgtcacctccatcctcactcaggaccctc -cgtgagtgccagctctgtctaccctcgggaccctccatgagtgtctcctctatctaccct -caggaccctctgtgaatgtcctcgccatccatactcccccctcttagacccagactgttt -cagggttggacactgagctgtggcccctgagcctagctcttctccgagcttctcttgggc -acctctctctcagactaggc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f6191264629ab8d6b67a342e9f6525b2.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f6191264629ab8d6b67a342e9f6525b2.msa deleted file mode 100644 index e9ec65cd..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f6191264629ab8d6b67a342e9f6525b2.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:23155468-23155967 -gcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgc -agcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggggagg -ggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggg -gggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaaagaa -gaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaaggaa -aggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaagagaga -aagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaagga -agaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaagagaa -agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaa -aagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaa -gaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtct -taacaccttggtaattttt ->syndip_2_chr20:23155468-23155967 -gcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgc -agcacaaaagaggaaggaaagcaag-------------------ggaagggaaggggagg -ggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggg -gggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaaagaa -gaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaaggaa -aggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaagagaga -aagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaagga -agaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag---- -----agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaa -aagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaa -gaaag------------------------aagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtct -taacaccttggtaattttt ->p:HG002_1_chr20:23155468-23155967 -gcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgc -agcacaaaagaggaaggaaagcaag-------------------ggaagggaaggggagg -ggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggg -gggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaaagaa -gaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaaggaa -aggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaagagaga -aagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaagga -agaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag---- -----agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaa -aagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaa -gaaag--------------------aagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtct -taacaccttggtaattttt ->p:HG002_2_chr20:23155468-23155967 -gcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgc -agcacaaaagaggaaggaaagcaagggaagggaaggggaggggaggaagggaaggggagg -ggaggaagggaaggggaggggaggaaggcgaggtgaggggaggagaggtgaggggagggg -gggaggggaggggagggagagtgaggaagagagagagaaagggagagaggaaggaaagaa -gaaaggaaggaaggaaagaaggaaggaagggagggagggagggaggaaagaaggaaggaa -aggagggaggaagggagggaaagagagagagaggaaaagagagagaaagagaaagagaga -aagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaagga -agaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaagagaa -agaaagaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaa -aagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaa -gaaagaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtct -taacaccttggtaattttt ->ref_chr20:23155468-23155967 -gcttttgcagtcatgattgatgcaggcagcacccttctgcagaagtaaattttgccctgc -agcacaaaagaggaaggaaagcaag-------------------ggaagggaaggggagg -ggaggaaggga------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------aggaaaagagagagaaagagaaagagaga -aagagaggaaggaaggaaggaaggagagagagaaagaaagaaggaaagaggaaggaagga -agaaagaaaagaaagaaagaaaaaagaaagaaaggaaggagagaaagaaatgaaag---- -----agaaagaaagaaagaaagaaagaaaggagagaaaaaggaaaaacaaagaaagagaa -aagaaggagagaaggaaaggaaaaagaaagaaagaaggaaagaaagaaaaaagaaggaaa -gaaag------------aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaag -aaagaaagaaagaaagaaagaaagaaaaagaaagagaaaggaaggaaggaaggaaggtct -taacaccttggtaattttt diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f6aa67e07aeaa28531bbe9e61e1085a1.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f6aa67e07aeaa28531bbe9e61e1085a1.msa deleted file mode 100644 index 64300342..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f6aa67e07aeaa28531bbe9e61e1085a1.msa +++ /dev/null @@ -1,95 +0,0 @@ ->syndip_1_chr20:63221379-63221977 -ctcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccg -atgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcat -cgcagtagcttc------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------ggactgcagggactgcaggga -ttgcagggactgcagggattgcagggactgcagggattgcagggattgcagggattgcag -ggattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacac -cttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctgg -tgaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcgg -ggccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcac -ct ->syndip_2_chr20:63221379-63221977 -ctcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccg -atgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcat -cgcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcaggga -gtgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgcag -ggactgcagggactgcagggactgcagggattgcagggactgcagggactgcagggattg -cagggattgcagggactgcagggactgcagggattgcagggactgcagggactgcaggga -ctgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcag -ggattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactg -cagggattgcagggattgcagggattgcagggattgcagggattgcagggactgcaggga -ctgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcag -ggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattg -cagggattgcagggactgcagggactgcagggactgcagggattgcagggattgcaggga -ttgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgcag -ggattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggacac -cttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctgg -tgaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcgg -ggccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcac -ct ->p:HG002_1_chr20:63221379-63221977 -ctcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccg -atgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcat -cgcagtagcttcggactgcagggattgcagggactgcagggattgcagggattgcaggga -gtgcagggactgcagggactgcagggattgcagggactgcagggactgcagggactgcag -ggactgcagggactgcagggactgcagggattgcagggactgcagggactgcagggattg -cagggattgcagggactgcagggactgcagggattgcagggactgcagggactgcaggga -ctgcagggactgcagggactgcagggactgcagggattgcagggattgcagggattgcag -ggattgcagggactgcagggactgcagggactgcagggactgcagggactgcagggactg -cagggattgcagggattgcagggattgcagggattgcagggattgcagggactgcaggga -ctgcagggactgcagggactgcagggattgcagggattgcagggattgcagggattgcag -ggactgcagggactgcagggattgcagggattgcagggattgcagggattgcagggattg -cagggattgcagggactgcagggactgcagggactgcagggattgcagggattgcaggga -ttgcagggattgcagggactgcagggactgcagggattgcagggattgcagggattgcag -ggattgcagggactgcagggcctgcattgctcttgcagcaccacccgcctccgtggccac -cttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctgg -tgaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcgg -ggccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcac -ct ->p:HG002_2_chr20:63221379-63221977 -ctcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccg -atgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcat -cgcagtagcttc------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------ggactgcagggactgcaggga -ttgcagggactgcagggattgcagggactgcagggattgcagggattgcagggattgcag -ggattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggccac -cttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctgg -tgaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcgg -ggccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcac -ct ->ref_chr20:63221379-63221977 -ctcccactgcagagaactgtcatctgcctgtaagtaccagtgccaggtgctctggggccg -atgtctccgttagccccaaggtggaggctcagggagcagatgtgagcgtgccttgctcat -cgcagtagcttc------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------ggactgcagggattgcagggactgcagggattgcagggattgcag -ggattgcagggactgcagggattgcagggactgcagggactgcagggactgcagggactg -cagggactgcagggattgcagggattgcagggattgcagggactgcagggattgcaggga -ctgcagggactgcagggattgcagggactgcagggactgcagggactgcagggattgcag -ggattgcagggactgcagggactgcattgctcttgcagcaccacccgcctccgtggacac -cttcagcagtgagacaatgcaggctctgctacaagaggtgcttactgggctctgctctgg -tgaggagaggcctcgcctggcagccagacagagtcccagcagggcaagatgaaaattcgg -ggccctcgttcaaacagcaagagaaggctctttccttccttccagcgcccctccctgcac -ct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f80b3949aaede63b2c726a14abd6e835.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f80b3949aaede63b2c726a14abd6e835.msa deleted file mode 100644 index 0379a39e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f80b3949aaede63b2c726a14abd6e835.msa +++ /dev/null @@ -1,100 +0,0 @@ ->syndip_1_chr20:61289525-61290655 -tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc -ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata -tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccg-------------------------------ta -tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg -tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tcccgatatccaatgagacttgctggatttatccccgtatccaatgagacttgctggg-- ------------------------------tttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg -gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc -tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt -gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca -cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc ->syndip_2_chr20:61289525-61290655 -tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc -ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata -tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccccta -tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg -tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg-- ------------------------------tttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg -gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc -tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt -gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca -cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc ->p:HG002_1_chr20:61289525-61290655 -tctgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc -ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata -tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatcccccta -tccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccccg -tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctggg-- ------------------------------tttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg -gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc -tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt -gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca -cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc ->p:HG002_2_chr20:61289525-61290655 -tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc -ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata -tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccg-------------------------------ta -tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg -tatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tcccgatatccaatgagacttgctggatttatccccgtatccaatgagacttgctggg-- ------------------------------tttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg -gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc -tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt -gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca -cagaggaaattgatggcttggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc ->ref_chr20:61289525-61290655 -tgtgtgggtgcccaggggcatgagtgcctggggagtgtgaccacaggccagtggcagtcc -ctgcctttggattaaagagccctttgaggcttgcttggtgatgtcatggaaaacagcata -tgacaccaagatatccccatatccaacgagacttgctgggtttatccccgtatccaacga -gacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatccaac -gagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatcca -acgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgtatc -caacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccgta -tccaacgagacttgctgggtttatccccgtatccaacgagacttgctgggtttatccccg -tatccaacgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatccc -cgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtttatc -cccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggttta -tccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgctgggtt -tatcccgatatccaatgagacttgctggatttatccccgtatccaatgagacttgctggg -tttatccccgtatccaatgagacttgctgggtttatcccgatatccaatgagacttgctg -gatttatccccgtatccaatgagacttgctgggtttatccccgtatccaatgagacttgc -tgggtttatcccgatatccaatgagacttgctggatttatccccgtatccaatgagactt -gctggatttatccccatatccaatgagacttgctgggtttagcaccacagatgccagtca -cagaggaaattgatggcatggcagacagcgtgacatgttgactacctgccctggtccttg -cagatggcatgggcacaaaggggatgtggggtgaagagttgaaacgagtgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f823e9dbba42cacbf8fab885e0cbd994.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f823e9dbba42cacbf8fab885e0cbd994.msa deleted file mode 100644 index f0ff1bd4..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f823e9dbba42cacbf8fab885e0cbd994.msa +++ /dev/null @@ -1,45 +0,0 @@ ->syndip_1_chr20:45600545-45600805 -ttaaaaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctc -tctcttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctc -tctctctctctctctctctctctctctctctatccccccctccctccctccttccctccc -tccctctctctctctctctccctttctctgtctctccctctctctctctctctctccctc -tctctctctttctccctctctctccctctctctctctctctctccctctctctctctttc -tccctctctctccctctctccccctctctctccctctctccctctctccctctctctccc -tctctctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatact -atactgagctacactaaagtttctatatttagccaaatccagc ->syndip_2_chr20:45600545-45600805 -ttaaaaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctc -tctcttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctc -tctc--tctctctctctctctctctctctctatccccccctccctccctccttccctccc -tccctctctctctctctctccctttctctgtctctccctctctctctctctctctccctc -tctct------------------------------------------------------- ----------------------ccctctctccccctctctctccctctctccctctctccc -tctctctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatact -atactgagctacactaaagtttctatatttagccaaatccagc ->p:HG002_1_chr20:45600545-45600805 -ttaaaaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctc -tctcttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctc -tctc--tctctctctctctctctctctctctatccccccctccctccctccttccctccc -tccctctctctctctctctccctttctctgtctctccctctctctctctctctctccctc -tctct------------------------------------------------------- ----------------------ccctctctccccctctctctccctatccccccctctccc -tctctctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatact -atactgagctacactaaagtttctatatttagccaaatccagc ->p:HG002_2_chr20:45600545-45600805 -ttaaaaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctc -tctcttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctc -tctctctctctctctctctctctctctctctatccccccctccctccctccttccctccc -tccctctctctctctctctccctttctctgtctctccctctctctctctctctctccctc -tctctctctttctccctctctctccctctctctctctctctctccctctctctctctttc -tccctctctctccctctctccccctctctctccctctctccctctatccccccctctccc -tctctctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatact -atactgagctacactaaagtttctatatttagccaaatccagc ->ref_chr20:45600545-45600805 -ttaaaaatcatctctttatctttcctaaatattccactgtctttgactgctatacctctc -tctcttttctttcaccaagcctctctctttgctttccttctggtaaaagcagtctctctc -tctc--tctctctctctctctct------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------ctatccccccctctccc -tctctctctacccctgaatctggcctttctaaacaccctcaacttgtgtacctgtatact -atactgagctacactaaagtttctatatttagccaaatccagc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f8e920b14bb9f31cfcc150d515f579de.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f8e920b14bb9f31cfcc150d515f579de.msa deleted file mode 100644 index 6b6a47e8..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f8e920b14bb9f31cfcc150d515f579de.msa +++ /dev/null @@ -1,70 +0,0 @@ ->syndip_1_chr20:44763795-44764386 -tgactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggt -tgcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacggg -ttccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatc -catccatccacctatcacttcatccatccatccatttatccatccatccatttatccatc -catccatccatttatccatccatccatccatttatccatccatccatccatccatccacc -catccatccgtccatccatttatccatccatccatccatccatttatccatccatttatc -catccatccatccatccatccatccatccatccatttatcc----atccatccatccatc -cacccatccatccatccgtccatccatttatccatccatccatccatccatccatccatc -catccatttatccatccgtccatttatccatccatccatccacccacccatccatccatc -catccacttatccatccacccatccatccatccgtccatccattcatccatccatccatc -ctcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacat -ttctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaa -atggggtcagtg ->syndip_2_chr20:44763795-44764386 -tgactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggt -tgcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacggg -ttccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatc -catccatccacctatcacttcatccatccatccatttatccatccatccatttatccatc -catccatccatttatccatccatccatccatttatccatccatccatccatccatccacc -catccatccgtccatccatttatccatccatccatccatccatttatccatccatttatc -catccatccatccatccatccatccatccatccatccatccatttatccatccatccatc -catccacccatccatccatccgtccatccatttatccatccatccatccatccatccatc -catccatttatccatccgtccatttatccatccatccatccacccacccatccatccatc -catccatttatccatccacccatccatccatccgtccatccattcatccatccatccatc -ctcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacat -ttctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaa -atggggtcagtg ->p:HG002_1_chr20:44763795-44764386 -tgactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggt -tgcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacggg -ttccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatc -catccatccacctatcacttcatccatccatccatttatccatccatccatttatccatc -catccatccatttatccatccatccatccatttatccatccatccatccatccatccacc -catccatccgtccatccatttatccatccatccatccatccatttatccatccatttatc -catccatccatccatccatccatccatccatccatccatccatttatccatccatccatc -catccacccatccatccatccgtccatccatttatccatccatccatccatccatccatc -catccatttatccatccgtccatttatccatccatccatccacccacccatccatccatc -catccatttatccatccacccatccatccatccgtccatccattcatccatccatccatc -ctcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacat -ttctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaa -atggggtcagtg ->p:HG002_2_chr20:44763795-44764386 -tgactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggt -tgcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacggg -ttccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatc -catccatccacctatcacttcatccatccatccatttatccatccatccatttatccatc -catccatccatttatccatccatccatccatttatccatccatccatccatccatccacc -catccatccgtccatccatttatccatccatccatccatccatttatccatccatttatc -catccatccatccatccatccatccatccatccatttatcc----atccatccatccatc -cacccatccatccatccgtccatccatttatccatccatccatccatccatccatccatc -catccatttatccatccgtccatttatccatccatccatccacccacccatccatccatc -catccacttatccatccacccatccatccatccgtccatccattcatccatccatccatc -ctcccacaaactcaccaagcctacaatacaatcaattctgctgtaacatgaaatatacat -ttctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaa -atggggtcagtg ->ref_chr20:44763795-44764386 -tgactccattctcttttccagatggatcactcgtctcaacagcatcagaaattaaaaggt -tgcacagcccttgtggtgattataggttatgtgattctcaaaggtttaggagtttacggg -ttccctgtccatccattcactacatgctcacctatccatccatccatccatttatccatc -catccatccacctatcacttcatccatccatccatttatccatccatccatttatccatc -catccatccatttatccatccatccatccatttatccatccatccatccatccatccacc -catccatccgtccatccatttatccatccatccatccatccatttatgcatccatttatc -catccatccatccatccatccatccatccatccatttatcc------------------- ------------------------------------------------------------- ------------------------------------------------------------- --atccatccatccatccacccatccatccatccgtccatccattcatccatccatccatc -ctcccacaaactcaccaagcctacaatgcaatcaattctgctgtaacatgaaatatacat -ttctaaaaattactgtgcaacgcaaaatcttgctataaaaatcacacagcttatgggaaa -atggggtcagtg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_f9e18489a12fd0cbbec25e9e7f481717.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_f9e18489a12fd0cbbec25e9e7f481717.msa deleted file mode 100644 index f37ac94e..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_f9e18489a12fd0cbbec25e9e7f481717.msa +++ /dev/null @@ -1,55 +0,0 @@ ->syndip_1_chr20:62830540-62830807 -ccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccc -tctcagcaggaagctcccctgcaccccctctacccatgtaccacagtcccccaccccc-- -caccgtgctccaccccccaccacagtcccccaccccccaccccagtccccaaacccctac -cacagtcccccaaccccaccacagtcccccaccccctaccacagtcccccaccccctacc -acagtcccccaacccccaccacagtcccccacccccaccacagtccgccaacccccatga -cagtccctcaacccccaccacagtcccccaacccccatgacagtcccccaacccccacca -cagtcccccaacccccaccacagt-ccccaccccctaccacagtcccccaacccccacca -cagtcccccaccccctaccacaatcccccaccccccaccacagtccc------------- ------------------------------------------------------------- ------- ->syndip_2_chr20:62830540-62830807 -ccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccc -tctcagcaggaagctcccctgcaccccctctacccatgtaccacagtccc---------- ----------ccaccccccaccacagtcccccaccccccaccccagtccccaaacccctac -cacagtcccccaaccccaccacagtcccccaccccctaccacagtcccccaacccctacc -acagtcccccaacccccaccacagtcccccacccccaccacagtccgccaacccccatga -cagtcccccaacccccaccacagtccccc-acccccaccacagtccgccaacccccatga -cagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaacccccacca -cagtcccccaacccctaccacagtcccccaacccccaccacagtccccaccccctaccac -agtcccccaacccccaccacagtcccccaccccctaccacaatcccccaccccccaccac -agtccc ->p:HG002_1_chr20:62830540-62830807 -ccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccc -tctcagcaggaagctcccctgcaccccctctacccatgtaccacagtccc---------- ----------ccaccccccaccacagtcccccaccccccaccccagtccccaaacccctac -cacagtcccccaaccccaccacagtcccccaccccctaccacagtcccccaacccctacc -acagtcccccaacccccaccacagtcccccacccccaccacagtccgccaacccccatga -cagtcccccaacccccaccacagtccccc-acccccaccacagtccgccaacccccatga -cagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaacccccacca -cagtcccccaacccctaccacagtcccccaacccccaccacagtccccaccccctaccac -agtcccccaacccccaccacagtcccccaccccctaccacaatcccccaccccccaccac -agtccc ->p:HG002_2_chr20:62830540-62830807 -ccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccc -tctcagcaggaagctcccctgcaccccctctacccatgtaccacagtcccccaccccc-- -caccgtgctccaccccccaccacagtcccccaccccccaccccagtccccaaacccctac -cacagtcccccaaccccaccacagtcccccaccccctaccacagtcccccaccccctacc -acagtcccccaacccccaccacagtcccccacccccaccacagtccgccaacccccatga -cagtcccccaacccccaccacagtcccccaacccccatgacagtcccccaacccctacca -cagtcccccaacccccaccacagt-ccccaccccctaccacagtcccccaacccccacca -cagtcccccaccccctaccacaatcccccaccccccaccacagtccc------------- ------------------------------------------------------------- ------- ->ref_chr20:62830540-62830807 -ccccggccttccaggcccccagggcctccgaggtgacgtgggcgaccgggtaagtggccc -tctcagcaggaagctcccctgcaccccctctacccatgtaccacagtcccccacccccat -gacagtcccccaacccccaccacagtcccccaacccctaccacagtcccccaacccccac -cacagtccccaccccctaccacagtcccccaacccccaccacagtcccccaccccctacc -acaatcccccaccccccaccacagtccc-------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------- diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fb52ef3187571c67509303c4c8e9c08d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fb52ef3187571c67509303c4c8e9c08d.msa deleted file mode 100644 index d35585ef..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fb52ef3187571c67509303c4c8e9c08d.msa +++ /dev/null @@ -1,75 +0,0 @@ ->syndip_1_chr20:41196110-41196748 -agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt -atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca -tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa -taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata -tatatcttataaatatatatatttatataacataaatatatatttatatatattata--- ----------------------aatatatattatatataatatatatttatataaatatat -atattatatataatatatttatatataatatatatttatatattataaatatatattata -tataatatatatttatataaatatatattatatataaatatatattatatataatatata -tttatataaatatatattatatattatataaatattatatataatatatatttatataaa -tatatattatatattataaatatatattatatattatatattatataaatattatatata -atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc -aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt -ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcc ->syndip_2_chr20:41196110-41196748 -agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt -atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca -tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa -taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata -tatatcttataaatatatatatttatataacataaatatatatttatatatattatataa -cataaatatatatttatatatattatatattatatataatatatatttatataaatatat -atattatatataatatatttatatataatatatatttatatattataaatatatattata -tataatatatatttatataaatatatattatatat------------------------- -----tataaatatatattatatattatataaatattatatataatatatatttatataaa -tatataatatatattataaatatatattatatattatatattatataaatattatatata -atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc -aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt -ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcc ->p:HG002_1_chr20:41196110-41196748 -agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt -atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca -tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa -taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata -tatatcttataaatatatatatttatataacataaatatatatttatatatattatataa -cataaatatatatttatatatattatatattatatataatatatatttatataaatatat -atattatatataatatatttatatataatatatatttatatattataaatatatattata -tataatatatatttatataaatatatattatatat------------------------- -----tataaatatatattatatattatataaatattatatataatatatatttatataaa -tatataatatatattataaatatatattatatattatatattatataaatattatatata -atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc -aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt -ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcc ->p:HG002_2_chr20:41196110-41196748 -agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt -atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca -tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa -taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata -tatatcttataaatatatatatttatataacataaatatatatttatatatattata--- ----------------------aatatatattatatataatatatatttatataaatatat -atattatatataatatatttatatataatatatatttatatattataaatatatattata -tataatatatatttatataaatatatattatatataaatatatattatatataatatata -tttatataaatatatattatatattatataaatattatatataatatatatttatataaa -tatatattatatattataaatatatattatatattatatattatataaatattatatata -atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc -aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt -ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcc ->ref_chr20:41196110-41196748 -agagtgttgttgaaatcctctatttcctgattgatcttctgtctggtttctatatccatt -atcggacatggaatattaaagtctccaactatttttgtctttctccctttaattctgtca -tttctgtttcatatgttttggagctctgttaggggtatatatatatataatatatataaa -taaatatataaaaataaatatatatttataataaatatatttttatttcatatataaata -tatatcttataaatatatatatttatataacataaatatatatttatatat--------- ----------------------attatatattatatataatatatatttatataaatatat -atattatatataatatatttatatataatatatatttatatattataaatatatat---- ------------------------------------------------------------- ------------------------------------------------------------- --------tatatattataaatatatattatatattatatattatataaatattatatata -atatatattatatataatatatataaaaatatatatatttatatatataaatattttatc -aatataatatccttgtctcttgtaacctttcttgatttaacatttattttgtgtgccttt -ttcaaaagaggacactggaggtgaagaaggaagctcttgactctcctaaagctgatccca -aagtgaaggctttgaaggcc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fd198272bc91bdb42e2dbb32cc9c9935.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fd198272bc91bdb42e2dbb32cc9c9935.msa deleted file mode 100644 index d7d2eb13..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fd198272bc91bdb42e2dbb32cc9c9935.msa +++ /dev/null @@ -1,385 +0,0 @@ ->syndip_1_chr20:63167287-63167727 -aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg -ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacggt -tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc -agtgcccacctcagccccctcctcagcccccacctccgcccccacctcagcccct----- --------------------cctcagcccccacctcagccccctcctcagcccccacctcc ------------------------gcccccacctccgcccccacctctgcccct------- -------cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccg -cccccacctctgcccct-------------------------------------cctcag -cccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctg -cccctcctcagcccccacctcagccccctcctcag-----------cccccacctccgcc -ccctcctcagcccccacctctgcccct------------cctcagcccccacctcagccc -cctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgcccc -cacctcagcccccacctcc-----------------------gccccctcctcagccccc -acctctgcccctcctcagcccccacctcagcccccacctcagcccccacctc-------- ------------------------------------------------------------- -----------------------------ccccctcctcagcccccacctcagcccccacc -tcagccccctcctcagcccccacctcagcccccacctccgcccct------------cct -cagcccccacctccgcccccacctcagcccccacctcagcccccacctccgcccccacct -cagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacct -ctgcccctcctcagcccccacctccgccccctcctcagcccccacctctg---------- ---------------------------cccctcctcagcccccacctcagcccccacctca -gcccccacctcc-cccctcctcagcccccacctcagcccccacctcagccccctcctcag -cccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagc -ccccacctccgcccctcctcagcccccacctcag-------------------------- ------------------------------------------------------------- ---------ccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc -tcctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgccccc -acctccgcccctcctccgcccccacctcagcccccacctccgccccct------------ -----------------------cctcagcccccacctctgcccctcctcagcccccacct -cagcccccacctcagcccccacct-------------------------cccccctcctc -agcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccca----- -------------------------------------------------------cctcag -cccccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcag -cccccacctcc-----------gcccccacctcagcccccacctctgcccctcctcagcc -cccacctccgccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc -ccacctcagcccccacct-------------------------cccccctcctcagcccc -ca-----------------------------------cctcagcccccacctcagccccc -tcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca ------------------------cctcagcccccacctccgcccctcctccgcccccacc -tcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacct -ccgcccccacctcagccccctcctcagcccccacctc----------------------- ---------------ccccctcctccgcccccacctcagcccccacctcagcccccacctc -agcccccacctc------------------------------------------------ ------------------------------------------------------------c -cccctcctccgcccccacctcagccccca-----------cctcagcccccacctccgcc -cccacctcagcccccacctcc--------------------------------------- ------------------------------------------------------------- --------cccctcctcagcccccacctcagcccccacctccgccccca-----------c -ctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacc -tccgcccccacctcagcccccacctcagcccccacctccgccccca-------------- --------------------------------------------------------cctca -gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc -gcccccacctccgcccccacctcc-----------gcccccacctcagcccccacctcag -cccccacctccgccccca------------------------------------------ -----cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccc -ccacctcagcccctcctcagcccccacctcagcccccacctcagcccccacctcagcccc -t-------------------------cctcagcccccacctcagccccctcctcagcccc -ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc -acctcagcccctcctcagcccccacctcagccc--------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------cctcagccccca -cctcagcccccacctccgcccccacctccgcccccacctcc------------------- ------------------------------------------------------------- -----gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct -cc---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------acccccacctccgtccccacctccgccccctcctcagccccctcctcagc -ccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgcc -cccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagctg -ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc -cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttg ->syndip_2_chr20:63167287-63167727 -aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg -ctatccatcccctcgactaatacttaccaaattaattccagatttggattcactcacggt -tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc -agtgcccacctcagccccctcctcagcccccacctccgcccccacctccgccccctcctc -agcccctcctccgcccccacctcagcccccacctcagccccctcctcagcccccacctcc -gcccctcctcagcccccacctcagcccccacctcagcccccacctccgccccctcctcag -cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctccg -cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcag -cccccacctcagccccctcctcagcccccacctcagcccccacctccgccccctcctcag -cccccacctcccccccacctccgccccctcctcagcccccacctcccccccacctccgcc -ccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctcagccc -cctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccc -cacctcagcccccacctccgcccctcctctgcccccacctcagccccctcctcagccccc -acctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagccccca -cctcagcccccacctccccccctcctcagcccccacctccacccccacctcagcccccac -ctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacc -tccgcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacct -cagcccccacctccgcccccacctccgcccccacctcagcccccacctccgccccctcct -cagcccccacctcagcccccacctcagcccccacctccacccccacctcagcccccacct -cagcccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctca -ggccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctca -gcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcag -cccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcagc -ccccacctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcc -cctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagccc -ccacctccccccctcctcagcccccacctccacccccacctcagcccccacctccgcccc -tcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgccccc -acctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccccac -ctccgcccctcctcagcccccacctcagcccccacctccgcccctcctcagcccccacct -cagcccccacctccacccccacctcagcccccacctcagcccccacctcccccccacctc -cgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctca -gccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcag -cccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacctcag -cccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgcc -cccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc -ccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcagcccc -cacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagccccc -acctccacccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca -cctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccacc -tccgcccccacctcagccccctcctccgcccctcctcagcccccacctccacccccacct -cagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacctc -agcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacctc -agccccctcctccacccctcctcagcccccacctccgcccccacctcagcccccacctcc -gcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcctcagc -ccccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctccgcc -cccacctcagcccccacctccgcccctcctcagcccccacctccacccccacctcagccc -ccacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagccccc -acctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccccccctc -ctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacc -tcagcccccacctccacccccacctcagcccccacctcagcccccacctccgcccctcct -cagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctca -gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc -gcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcag -accccacctccgcccccacctccgcccctcctcagcccccacctcagcccccacctcagc -ccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctcagccc -ccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagcccc -cacctcagcccccacctccgcccccacctcagccccctcctcagcccccacctcagcccc -ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc -acctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcc -tcagcccccacctcagccccctcagcccccacctcagcccccacctccgcccccacctcc -gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgc -ccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctcagcc -ccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctcagccc -ctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcctcagccccca -cctcagcccccacctccgcccccacctccgcccccacctccgcccccacctcagcccctc -ctcagcccccacctcagcccccacctcagccccctcctcagcccccacctccgcccccac -ctcagcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct -ccgcccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctc -agccccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctca -gcccctcctcagcccccacctcagcccctcctcagccccctcctcagcccccacctcagc -ccccacctcagcccccacctccgcccccacctccgcccccacctcagccccctcctcagc -cccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgcc -cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg -ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc -cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttg ->p:HG002_1_chr20:63167287-63167727 -aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg -ctatccatcccctcgactaatacttaccaaattaattccagatttggattcactcacggt -tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc -agtgcccacctcagccccctcctcagcccccacctccgcccccacctccgccccctcctc -agcccctcctccgcccccacctcagcccccacctcagccccctcctcagcccccacctcc -gcccctcctcagcccccacctcagcccccacctcagcccccacctccgccccctcctcag -cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctccg -cccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctcag -cccccacctcagccccctcctcagcccccacctcagcccccacctccgccccctcctcag -cccccacctcccccccacctccgccccctcctcagcccccacctcccccccacctccgcc -ccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctcagccc -cctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccc -cacctcagcccccacctccgcccctcctctgcccccacctcagccccctcctcagccccc -acctctgcccctcctcagcccccacctcagcccccacctccgcccccacctcagccccca -cctcagcccccacctccccccctcctcagcccccacctccacccccacctcagcccccac -ctcagcccccacctccccccctcctcagcccccacctccgcccccacctcagcccccacc -tccgcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacct -cagcccccacctccgcccccacctccgcccccacctcagcccccacctccgccccctcct -cagcccccacctcagcccccacctcagcccccacctccacccccacctcagcccccacct -cagcccccacctcccccccacctccgccccctcctcagcccccacctctgcccctcctca -ggccccacctcagcccccacctcagccccctcctcagcccccacctcagcccccacctca -gcccccacctccgcccctcctcagcccccacctcagcccccacctccacccccacctcag -cccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacctcagc -ccccacctccgcccctcctctgcccccacctcagccccctcctcagcccccacctctgcc -cctcctcagcccccacctcagcccccacctccgcccccacctcagcccccacctcagccc -ccacctccccccctcctcagcccccacctccacccccacctcagcccccacctccgcccc -tcctcagcccccacctcagcccccacctccacccccacctcagcccccacctccgccccc -acctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagcccccac -ctccgcccctcctcagcccccacctcagcccccacctccgcccctcctcagcccccacct -cagcccccacctccacccccacctcagcccccacctcagcccccacctcccccccacctc -cgccccctcctcagcccccacctctgcccctcctcaggccccacctcagcccccacctca -gccccctcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcag -cccccacctcagcccccacctccacccccacctcagcccccacctccgcccccacctcag -cccccacctccgcccctcctcagcccccacctcagcccccacctccgcccctcctctgcc -cccacctcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc -ccacctccgcccccacctcagcccccacctcagcccccacctccccccctcctcagcccc -cacctccacccccacctcagcccccacctccgcccctcctcagcccccacctcagccccc -acctccacccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca -cctccgcccccacctcagcccctcctcagcccccacctccgcccctcctcagcccccacc -tccgcccccacctcagccccctcctccgcccctcctcagcccccacctccacccccacct -cagcccccacctcagccccctcctcagcccccacctccgcccctcctcagcccccacctc -agcccccacctcagcccccacctccgccccctcctcagcccccacctcagcccccacctc -agccccctcctccacccctcctcagcccccacctccgcccccacctcagcccccacctcc -gcccctcctcagcccccacctccacccccacctcagcccccacctccgcccctcctcagc -ccccacctccgcccccacctcagcccccacctccccccctcctcagcccccacctccgcc -cccacctcagcccccacctccgcccctcctcagcccccacctccacccccacctcagccc -ccacctccgcccctcctcagcccccacctccgcccccacctcagcccctcctcagccccc -acctccgcccctcctcagcccccacctccgcccccacctcagcccccacctccccccctc -ctcagcccccacctccgcccccacctcagcccccacctccgcccctcctcagcccccacc -tcagcccccacctccacccccacctcagcccccacctcagcccccacctccgcccctcct -cagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcccctcctca -gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc -gcccccacctcagcccccacctccgcccctcctcagcccccacctcagcccccacctcag -accccacctccgcccccacctccgcccctcctcagcccccacctcagcccccacctcagc -ccctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctcagccc -ccacctcagcccctcctcagcccccacctcagcccccacctcagccccctcctcagcccc -cacctcagcccccacctccgcccccacctcagccccctcctcagcccccacctcagcccc -ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc -acctcagcccctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcc -tcagcccccacctcagccccctcagcccccacctcagcccccacctccgcccccacctcc -gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgc -ccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctcagcc -ccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctcagccc -ctcctcagcccccacctcagcccctcctcagcccccacctcagcccctcctcagccccca -cctcagcccccacctccgcccccacctccgcccccacctccgcccccacctcagcccctc -ctcagcccccacctcagcccccacctcagccccctcctcagcccccacctccgcccccac -ctcagcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct -ccgcccccacctccgcccccacctcagcccctcctcagcccccacctcagcccccacctc -agccccctcctcagcccccacctccgcccccacctccgcccccacctcagccccacctca -gcccctcctcagcccccacctcagcccctcctcagccccctcctcagcccccacctcagc -ccccacctcagcccccacctccgcccccacctccgcccccacctcagccccctcctcagc -cccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacctccgcc -cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg -ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc -cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttg ->p:HG002_2_chr20:63167287-63167727 -aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg -ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcacggt -tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc -agtgcccacctcagccccctcctcagcccccacctccgcccccacctcagcccct----- --------------------cctcagcccccacctcagccccctcctcagcccccacctcc ------------------------gcccccacctccgcccccacctctgcccct------- -------cctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccg -cccccacctctgcccct-------------------------------------cctcag -cccccacctcagccccctcctcagcccccacctccgcccccacctccgcccccacctctg -cccctcctcagcccccacctcagccccctcctcag-----------cccccacctccgcc -ccctcctcagcccccacctctgcccct------------cctcagcccccacctcagccc -cctcctcagcccccacctccgcccccacctccgcccccacctccgcccctcctccgcccc -cacctcagcccccacctcc-----------------------gccccctcctcagccccc -acctctgcccctcctcagcccccacctcagcccccacctcagcccccacctc-------- ------------------------------------------------------------- -----------------------------ccccctcctcagcccccacctcagcccccacc -tcagccccctcctcagcccccacctcagcccccacctccgcccct------------cct -cagcccccacctccgcccccacctcagcccccacctcagcccccacctccgcccccacct -cagcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacct -ctgcccctcctcagcccccacctccgccccctcctcagcccccacctctg---------- ---------------------------cccctcctcagcccccacctcagcccccacctca -gcccccacctcc-cccctcctcagcccccacctcagcccccacctcagccccctcctcag -cccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacctcagc -ccccacctccgcccctcctcagcccccacctcag-------------------------- ------------------------------------------------------------- ---------ccccctcctcagcccccacctccgcccccacctccgcccccacctctgcccc -tcctcagcccccacctcagccccctcctcagcccccacctccgcccccacctccgccccc -acctccgcccctcctccgcccccacctcagcccccacctccgccccct------------ -----------------------cctcagcccccacctctgcccctcctcagcccccacct -cagcccccacctcagcccccacct-------------------------cccccctcctc -agcccccacctcagcccccacctccgcccctcctcagcccccacctccgccccca----- -------------------------------------------------------cctcag -cccccacctcagcccccacctccgcccccacctcagcccccacctccgcccccacctcag -cccccacctcc-----------gcccccacctcagcccccacctctgcccctcctcagcc -cccacctccgccccctcctcagcccccacctctgcccctcctcagcccccacctcagccc -ccacctcagcccccacct-------------------------cccccctcctcagcccc -ca-----------------------------------cctcagcccccacctcagccccc -tcctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccccca ------------------------cctcagcccccacctccgcccctcctccgcccccacc -tcagccccctcctcagcccccacctctgcccctcctcagcccccacctcagcccccacct -ccgcccccacctcagccccctcctcagcccccacctc----------------------- ---------------ccccctcctccgcccccacctcagcccccacctcagcccccacctc -agcccccacctc------------------------------------------------ ------------------------------------------------------------c -cccctcctccgcccccacctcagccccca-----------cctcagcccccacctccgcc -cccacctcagcccccacctcc--------------------------------------- ------------------------------------------------------------- --------cccctcctcagcccccacctcagcccccacctccgccccca-----------c -ctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagcccccacc -tccgcccccacctcagcccccacctcagcccccacctccgccccca-------------- --------------------------------------------------------cctca -gcccccacctccgcccccacctcagcccccacctccgcccccacctcagcccccacctcc -gcccccacctccgcccccacctcc-----------gcccccacctcagcccccacctcag -cccccacctccgccccca------------------------------------------ -----cctcagcccccacctcagcccccacctcagcccccacctccgcccctcctcagccc -ccacctcagcccctcctcagcccccacctcagcccccacctcagcccccacctcagcccc -t-------------------------cctcagcccccacctcagccccctcctcagcccc -ctcctcagcccccacctcagcccccacctccgcccccacctccgcccccacctcagcccc -acctcagcccctcctcagcccccacctcagccc--------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -------------------------------------------------cctcagccccca -cctcagcccccacctccgcccccacctccgcccccacctcc------------------- ------------------------------------------------------------- -----gcccctcctcagcccccacctcagcccccacctcagcccctcctcagcccccacct -cc---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------acccccacctccgtccccacctccgccccctcctcagccccctcctcagc -ccccacctcagcccccacctccgcccccacctcagcccctcctcagcccccacctctgcc -cccacctcagaccctcctcagcccctcctcagcccctcctcatcccctcctcagcagctg -ctggaatgggctaccctcaggagttggcaccccacagcctccttcccttcccacctccgc -cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttg ->ref_chr20:63167287-63167727 -aatggccagcccgtcccgccgaggccagtggacatgccaaatccctcccgcaacaagttg -ctatccatcccctcgactaatacttaccaaattaattccagatttggagtcactcatggt -tcccaccagcactcagccccatctcagcccccatctcagcccccaccgcagcctcacctc -agtgcccacctcagccccctcctcagccccca---------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------cctcagcccccacctccgcccccacctcagcccctcctcagcccccacctccgcc -cccacctcaga-----------ccctcctcagcccctcctcatcccctcctcagcagctg -ctggaatgggctaccctcaggagttggcaccccacaggctccttcccttcccacctccgc -cacaccctgacgagggaaaaatggggagctgctgggagggaacttgcaccctgttgggcg -ccttg diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fd73fe09f67b4a93b56b114e8572636d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fd73fe09f67b4a93b56b114e8572636d.msa deleted file mode 100644 index 8f615dc2..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fd73fe09f67b4a93b56b114e8572636d.msa +++ /dev/null @@ -1,275 +0,0 @@ ->syndip_1_chr20:64125008-64128075 -gattacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgagg -tttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggc -ctcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagttt -tttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgc -ctggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatc -ttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatact -caaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatt -accaaagctttata-------------------------------ctcaaataccacact -gtcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttat -actcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttg -attaccacagctttatactcaaataccacactgtcttgattcctatagctttatactcaa -ataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaatactacactgtcttgattactatagctttatactcaaatacta -cactgtctgattactacagctttatactcaaataccaccctgtcttgattaccacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatact-------- -----------------------------acaccgtcttgattaccacagctgtatactca -aatactacactgtcttgattaccacagctttatactcaaataccacactgtcttgattac -caccgctttatactcaaataccacactgtcttgattactatagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactatagctttatactcaaatactacactgt -ctgattactacagctttatactcaaataccacactatcttgattactacagctttatact -caaatactacactgtctgattactacagctttatactcaaataccacaccgtcttgatta -ccacagctttatactcaaatactacactgtcttgattactacagctttatactcaaatac -cacaccgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccacag -ctttatactcaaatactacaccgtcttgattaccacagctttatactcaaataccacact -gtcttgattactatagctttatactcaaatactacactgtctgattactacagctttata -ctcaaataccacactgtcttgattaccacagctttatactcaaatactacactgtctgat -tactacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -actacactgtcttgattaccacagctttatactcaaataccacaccgtcttgattaccac -agctgtatactcaaataccacactgtcttgattaccacagctgtatactcaaataccaca -ctgtcttgattaccacagctttatactcaaatacc------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --acactgtcttgattaccacagctttatacgcaaataccacactgtcttgattactatag -ctttatactcaaataccacactgtcttgattactacagctttatactcaaataccacact -gtcttgattactacagctttatactcaaatactacactgtcttgattaacacagctttat -actcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttg -attactatagctttatactcaaataccacactgtcttgattactatagctttatactcaa -atactacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaataccacactgtcttgattaccac-------------------- ------------------------------------------------------------- -----------------------------------agctttatactcaaataccacactgt -cttgattaccacagctttatactcaaatactacactgtcttgattactac---------- ------------------------------------------------------------- -------agctttatactcaaatacc----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------acactgtcttgattactatagctttatactcaaataccacactgtct -tgattactatagctttatactctgttttgaggtcaggtagtgtcagtccctctaacttca -tttttcaaagttgttaggggattataggttctttgcaaatttctatgcaaattttggaat -cagtttgttaatttccagaaaaaagcctcttgc ->syndip_2_chr20:64125008-64128075 -gattacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgagg -tttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggc -ctcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagttt -tttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgc -ctggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatc -ttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatact -caaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatt -accaaagctttata-------------------------------ctcaaataccacact -gtcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttat -actcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttg -attaccacagctttatactcaaataccacactgtcttgattcctatagctttatactcaa -ataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaatactacactgtcttgattactatagctttatactcaaatacta -cactgtctgattactacagctttatactcaaataccaccctgtcttgattaccacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatact-------- -----------------------------acaccgtcttgattaccacagctgtatactca -aatactacactgtcttgattaccacagctttatactcaaataccacactgtcttgattac -caccgctttatactcaaataccacactgtcttgattactatagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactatagctttatactcaaatactacactgt -ctgattactacagctttatactcaaataccacactatcttgattactacagctttatact -caaatactacactgtctgattactacagctttatactcaaataccacaccgtcttgatta -ccacagctttatactcaaatactacactgtcttgattactacagctttatactcaaatac -cacaccgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccacag -ctttatactcaaatactacaccgtcttgattaccacagctttatactcaaataccacact -gtcttgattactatagctttatactcaaatactacactgtctgattactacagctttata -ctcaaataccacactgtcttgattaccacagctttatactcaaatactacactgtctgat -tactacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -actacactgtcttgattaccacagctttatactcaaataccacaccgtcttgattaccac -agctgtatactcaaataccacactgtcttgattaccacagctgtatactcaaataccaca -ctgtcttgattaccacagctttatactcaaatacc------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --acactgtcttgattaccacagctttatacgcaaataccacactgtcttgattactatag -ctttatactcaaataccacactgtcttgattactacagctttatactcaaataccacact -gtcttgattactacagctttatactcaaatactacactgtcttgattaacacagctttat -actcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttg -attactatagctttatactcaaataccacactgtcttgattactatagctttatactcaa -atactacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaataccacactgtcttgattaccac-------------------- ------------------------------------------------------------- -----------------------------------agctttatactcaaataccacactgt -cttgattaccacagctttatactcaaataccacactgtcttgattactac---------- ------------------------------------------------------------- -------agctttatactcaaatacc----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------acactgtcttgattactatagctttatactcaaataccacactgtct -tgattactatagctttatactctgttttgaggtcaggtagtgtcagtccctctaacttca -tttttcaaagttgttaggggattataggttctttgcaaatttctatgcaaattttggaat -cagtttgttaatttccagaaaaaagcctcttgc ->p:HG002_1_chr20:64125008-64128075 -gattacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgagg -tttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggc -ctcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagttt -tttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgc -ctggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatc -ttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatact -caaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatt -accaaagctttata-------------------------------ctcaaataccacact -gtcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttat -actcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttg -attaccacagctttatactcaaataccacactgtcttgattcctatagctttatactcaa -ataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaatactacactgtcttgattactatagctttatactcaaatacta -cactgtctgattactacagctttatactcaaataccaccctgtcttgattaccacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatact-------- -----------------------------acaccgtcttgattaccacagctgtatactca -aatactacactgtcttgattaccacagctttatactcaaataccacactgtcttgattac -caccgctttatactcaaataccacactgtcttgattactatagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactatagctttatactcaaatactacactgt -ctgattactacagctttatactcaaataccacactatcttgattactacagctttatact -caaatactacactgtctgattactacagctttatactcaaataccacaccgtcttgatta -ccacagctttatactcaaatactacactgtcttgattactacagctttatactcaaatac -cacaccgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccacag -ctttatactcaaatactacaccgtcttgattaccacagctttatactcaaataccacact -gtcttgattactatagctttatactcaaatactacactgtctgattactacagctttata -ctcaaataccacactgtcttgattaccacagctttatactcaaatactacactgtctgat -tactacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -actacactgtcttgattaccacagctttatactcaaataccacaccgtcttgattaccac -agctgtatactcaaataccacactgtcttgattaccacagctgtatactcaaataccaca -ctgtcttgattaccacagctttatactcaaatacc------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --acactgtcttgattaccacagctttatacgcaaataccacactgtcttgattactatag -ctttatactcaaataccacactgtcttgattactacagctttatactcaaataccacact -gtcttgattactacagctttatactcaaatactacactgtcttgattaacacagctttat -actcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttg -attactatagctttatactcaaataccacactgtcttgattactatagctttatactcaa -atactacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaataccacactgtcttgattaccac-------------------- ------------------------------------------------------------- -----------------------------------agctttatactcaaataccacactgt -cttgattaccacagctttatactcaaataccacactgtcttgattactac---------- ------------------------------------------------------------- -------agctttatactcaaatacc----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------acactgtcttgattactatagctttatactcaaataccacactgtct -tgattactatagctttatactctgttttgaggtcaggtagtgtcagtccctctaacttca -tttttcaaagttgttaggggattataggttctttgcaaatttctatgcaaattttggaat -cagtttgttaatttccagaaaaaagcctcttgc ->p:HG002_2_chr20:64125008-64128075 -gattacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgagg -tttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggc -ctcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagttt -tttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgc -ctggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatc -ttgattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatact -caaataccacaccgtcttgattaccacagctttatactcaaataccacaccgtcttgatt -accaaagctttata-------------------------------ctcaaataccacact -gtcttgattaccacagctttatactcaaataacacaccgtcttgattaccacagctttat -actcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttg -attaccacagctttatactcaaataccacactgtcttgattcctatagctttatactcaa -ataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaatactacactgtcttgattactatagctttatactcaaatacta -cactgtctgattactacagctttatactcaaataccaccctgtcttgattaccacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatact-------- -----------------------------acaccgtcttgattaccacagctgtatactca -aatactacactgtcttgattaccacagctttatactcaaataccacactgtcttgattac -caccgctttatactcaaataccacactgtcttgattactatagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactatagctttatactcaaatactacactgt -ctgattactacagctttatactcaaataccacactatcttgattactacagctttatact -caaatactacactgtctgattactacagctttatactcaaataccacaccgtcttgatta -ccacagctttatactcaaatactacactgtcttgattactacagctttatactcaaatac -cacaccgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccacag -ctttatactcaaatactacaccgtcttgattaccacagctttatactcaaataccacact -gtcttgattactatagctttatactcaaatactacactgtctgattactacagctttata -ctcaaataccacactgtcttgattaccacagctttatactcaaatactacactgtctgat -tactacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -actacactgtcttgattaccacagctttatactcaaataccacaccgtcttgattaccac -agctgtatactcaaataccacactgtcttgattaccacagctgtatactcaaataccaca -ctgtcttgattaccacagctttatactcaaatacc------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --acactgtcttgattaccacagctttatacgcaaataccacactgtcttgattactatag -ctttatactcaaataccacactgtcttgattactacagctttatactcaaataccacact -gtcttgattactacagctttatactcaaatactacactgtcttgattaacacagctttat -actcaaatactacactgtcttgattaccacagctttatactcaaatactacactgtcttg -attactatagctttatactcaaataccacactgtcttgattactatagctttatactcaa -atactacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaataccacactgtcttgattaccac-------------------- ------------------------------------------------------------- -----------------------------------agctttatactcaaataccacactgt -cttgattaccacagctttatactcaaatactacactgtcttgattactac---------- ------------------------------------------------------------- -------agctttatactcaaatacc----------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------acactgtcttgattactatagctttatactcaaataccacactgtct -tgattactatagctttatactctgttttgaggtcaggtagtgtcagtccctctaacttca -tttttcaaagttgttaggggattataggttctttgcaaatttctatgcaaattttggaat -cagtttgttaatttccagaaaaaagcctcttgc ->ref_chr20:64125008-64128075 -gattacaggtgtgcaccaccacacccagctaatttttttgtattttcagtagagatgagg -tttcactgtgttagccaggatggtctcgatttcctgacctcatgatccacccaccttggc -ctcccaaagtgctgggattacaggtgtgagccactgcgcccggacacactttgctagttt -tttttttttgttttgtttttttagtagcagtgctgggattacaggtgtcagccaccatgc -ctggctcaaatactacactgtcttgattactacagctttatactcaaatactacaccatc -ttgattactacagctt--------------------------------------tatact -caaataccacaccgtcttgattaccacagctgtatactcaaataccacaccgtcttgatt -accaaagctttatactcaaataccacactgtcttgattaccacagc-------------- ------------------tttatactcaaataacacaccgtcttgattaccacagctttat -actcaaatactacaccgtcttgattaccacagctttatactcaaataccacactgtcttg -attaccacagctttatactcaaatactacactgtcttgattcctatagctttatactcaa -ataccacactgtcttgattaccacagctttatactcaaatactacactgtcttgattact -atagctttatactcaaatactacactgtcttgattactatagctttatactcaaatacta -cactgtctgattactacagctttatactcaaataccaccctgtcttgattaccacagctt -tatactcaaataccacaccgtcttgattaccacagctgtatactcaaatactactgtcct -gattactacagctttatactcaaataccacaccgtcttgattaccacagctgtatactca -aatactacaccgtcttgattaccacagctttatactcaaatactacaccgtcttgattac -cacagctttatactcaaataccacactgtcttgattactatagctttatactcaaatact -acactgtctgattactacagctttatactcaaataccacactgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactatagctttatactcaaatactacactgt -ctgattactacagctttatactcaaataccacactatcttgattactacagctttatact -caaatactacactgtctgattactacagctttatactcaaataccacaccgtcttgatta -ccacagctttatactcaaatactacactgtcttgattactacagctttatactcaaatac -cacaccgtcttgattaccacagctgtatactcaaatactacaccgtcttgattaccacag -ctttatactcaaatactacaccgtcttgattaccacagctttatactcaaataacacact -gtcttgattactatagctttatactcaaatactacactgtctgattactacagctttata -ctcaaataccacactgtcttgattaccacagctttatactcaaatactacactgtctgat -tactacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -actacactgtcttgattaccacagctttatactcaaataccacaccgtcttgattaccac -agctgtatactcaaataccacactgtcttgattaccacagctgtatactcaaataccaca -ctgtcttgattaccacagctttatactcaaataccacactgtcttgattactatagcttt -atactcaaataccacactgtcttgattaccacagctttatacgcaaataccacactgtct -tgattactatagctttatactcaaataccacactgtcttgattactacagctttatactc -aaataccacactgtcttgattactacagctttatactcaaatactacactgtcttgatta -acacagctttatactcaaatactacactgtcttgattaccacagctttatactcaaatac -tacactgtcttgattactatagctttatactcaaataccacactgtcttgattactatag -ctttatactcaaatactacactgtcttgattaccacagctttatactcaaatactacact -gtcttgattact--------------------------------------atagctttat -actcaaataccacactgtcttgattaccac------------------------------ ---------agctttatactcaaataccacactgtcttgattaccacagctttatactcaa -ataccacactgtcttgattaccacagctttatactcaaataccacactgtcttgattact -atagctttatactcaaataccacactgtcttgattactacagctttatactcaaatacca -cactgtcttgattaacacagctttatactcaaatactacactgtcttgattaccacagct -ttatactcaaatactacactgtcttgattactatagctttatactcaaataccacactgt -cttgattactatagctttatactcaaatactacactgtcttgattaccacagctttatac -tcaaatactacactgtcttgattactatagctttgtactcaaataccacactgtcttgat -taccacagctttatactcaaataccacactgtcttgattaccacagctttatactcaaat -accacactgtcttgattactatagctttatactcaaataccacactgtcttgattactac -agctttatactcaaataccacactgtcttgattactacagctttatactcaaatactaca -ctgtcttgattaacacagctttatactcaaatactacactgtcttgattaccacagcttt -atactcaaatactacactgtcttgattactatagctttatactcaaataccacactgtct -tgattactatagctttatactctgttttgaggtcaggtagtgtcagtccctctaacttca -tttttcaaagttgttaggggattataggttctttgcaaatttctatgcaaattttggaat -cagtttgttaatttccagaaaaaagcctcttgc diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_fdcb2c8d04f052ec0422554bbca6ba2d.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_fdcb2c8d04f052ec0422554bbca6ba2d.msa deleted file mode 100644 index 761b2923..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_fdcb2c8d04f052ec0422554bbca6ba2d.msa +++ /dev/null @@ -1,165 +0,0 @@ ->syndip_1_chr20:60314230-60315120 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt -cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc -catttgtccttccttccttccttccttccttc---cttccttccttccttccttccttcc -ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacc -atcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatcc -atccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatcc -atcctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatcc -actcttccatccatccatccacccaccctt----------------ccatccatccatcc -tcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatcc -atcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcc -tcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcc -tcccatcctcccatccatccatccatcctcccatccgtccatccatccttccatccac-- ---------------cctcccatccatccatcctcccatccatctaccctcccatccatcc -atcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatct -atccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcct -cccataatctatcttcccatccatttgtccttccttccttccttccttccttccttcctt -cgttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaa -ccatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctat -ccat--------------------ccatcctcccatccatcctcccatcctcccatccat -tctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctc -ccatccatccatcctcccatccatccacccttccatccatccatccacccacccttccat -ccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctc -ccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccat -ccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccat -ccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccat -cctcccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccat -cgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccat -ccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccat -ccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgt -gagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaa -aatgaaaaaaagaatatattgatttcaggccagttacatag ->syndip_2_chr20:60314230-60315120 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt -cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc -catttg--------------------tccttc---cttccttccttccttccttccttcc -ttccacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaacc -atcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatcc -atccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatcc -atcctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatcc -acccttccatccatccatccacccacccttccatccatccatcctcccatccatccatcc -tcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatcc -atcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcc -tcccatccatctaccctcccatccatccatcctcccatccaccctcccatccatccatcc -atccatccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccc -tcccatccatccatcctcccatccatccatcctcccatccatctaccctcccatccatcc -atcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatct -atccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcct -cccataatctatcttcccatccatttgtccttccttccttccttccttccttcc------ ---ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaa -ccatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctat -ccatccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccat -tctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctc -ccatccatccatcctcccatccatccacccttccatccatccatccacccacccttccat -ccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctc -ccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccat -ccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccat -ccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccat -cctc----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccat -cgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccat -ccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccat -ccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgt -gagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaa -aatgaaaaaaagaatatattgatttcaggccagttacatag ->p:HG002_1_chr20:60314230-60315120 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt -cgtcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc -catttg--------------------tccttc---cttccttccttccttccttccttcc -ttccacccatccatcctcccatgcatcctcccatgcatcctcccatccatccacccaacc -atcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatcc -atccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatcc -atcctcctatccatccatccatccatccaccctctcatccatccatcctcccatccatcc -acccttccatccatccatccacccacccttccatccatccatcctcccatccatccatcc -tcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatcc -atcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcc -tcccatccatctaccctcccatccatccatcctcccatccaccctcccatccatccatcc -atccatccaccctctcatccatccatcctcccatccgtccatccatccttccatccaccc -tcccatccatccatcctcccatccatccatcctcccatccatctaccctcccatccatcc -atcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatct -atccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcct -cccataatctatcttcccatccatttgtccttccttccttccttccttccttcc------ ---ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaa -ccatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctat -ccatccatcctcccatccatcctcccatcctcccatccatcctcccatcctcccatccat -tctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctc -ccatccatccatcctcccatccatccacccttccatccatccatccacccacccttccat -ccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctc -ccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccat -ccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccat -ccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccat -cctc----ccatccatccatccatccatccatcctcccatcctcccatcctcccatccat -cgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccat -ccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccat -ccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgt -gagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaa -aatgaaaaaaagaatatattgatttcaggccagttacatag ->p:HG002_2_chr20:60314230-60315120 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt -cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc -catttgtccttccttccttccttccttccttc---cttccttccttccttccttccttcc -ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacc -atcctcccatccatcctcacatccatcttcgcatccatccatccatccatctatccatcc -atccatccatcctcccatccatcctcccatccattatcccattcatccatcctcccatcc -atcctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatcc -actcttccatccatccatccacccaccctt----------------ccatccatccatcc -tcccatccatccatcctcccattcatctatccatccatccctcgatcctcccatccatcc -atcctcccatccatccatccatcctcccatccatccatccaccctcccatccatccatcc -tcccatccatctaccctcccatccatccatcctcccacccaccctcccatccatccatcc -tcccatcctcccatccatccatccatcctcccatccgtccatccatccttccatccac-- ---------------cctcccatccatccatcctcccatccatctaccctcccatccatcc -atcctcccacccaccctcccatccatccaccctcccatccatccatcctcccatccatct -atccatccatcctcccatcctcccatccatccatcatccatccatccatccatccatcct -cccataatctatcttcccatccatttgtccttccttccttccttccttccttccttcctt -cgttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaa -ccatcctcccatccatcctcacatccatcttcgcatccatccatccatccatccatctat -ccat--------------------ccatcctcccatccatcctcccatcctcccatccat -tctcccattcatccatcctcccatccatcctcctatccatccatccatccatccaccctc -ccatccatccatcctcccatccatccacccttccatccatccatccacccacccttccat -ccatccaccctcccatccatccatcctcccattcatctatccatccatccctcgatcctc -ccatccatccatccatcctcccatccgtccatccatccttccatccaccctcccatccat -ccatcctcccatccatctaccctcccatccatccatcctcccacccaccctcccatccat -ccaccctcccatccatccatcctcccatccatctatccatccatcctcccatcctcccat -cctcccatccatccatccatccatccatccatcctcccatcctcccatcctcccatccat -cgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccat -ccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccat -ccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgt -gagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaa -aatgaaaaaaagaatatattgatttcaggccagttacatag ->ref_chr20:60314230-60315120 -acttgtttcctcatttattcattaacaatattcatttcttagccaaggatggtggtgcac -acctgtacttccagctactcaggaggctgaggtggaaggattgaaaatccatccatctgt -cctcctacccatcctgctatccatccatccatccatcctcccataatctatcttcccatc -catttgtccttccttccttccttccttccttccttcttccttccttccttccttccttcc -ttccacccatccatcctcccattcatcctcccatgcatcctcccatccatccacccaacc -atcctcccatccatcctcacatcgatcttcgcatccatccatcgatcgatctatccatcc -atccattc----------------------------tcccattcatccatcctcccatcc -atcctcctatccatccatccatccatccaccctcccatccatccatcctcccatccatcc -acccttccatccatccatccacccaccctt----------------ccatccatccaccc -tcccatccatccatcctcccatccatctatccatccatcctcccatcctcccatcctccc -at---------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------ccatccatccatccatccatccatcctcccatcctcccatcctcccatccat -cgtcccatgtgtacatctgtcctgccatctatccatacatccatttctccgtcctcccat -ccatcttcccatccattcatccatccatcttcccatccattcatccatccatcctgccat -ccatccttccattgatccatccatccatcctgcaggagaccaggagttcaaggctgccgt -gagttataattgtgccactgcactacagcttaagtgacagagagagaaaccatctccaaa -aatgaaaaaaagaatatattgatttcaggccagttacatag diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ff0ae7d50dec8afd13f0c22741c4925e.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ff0ae7d50dec8afd13f0c22741c4925e.msa deleted file mode 100644 index 55e2be1d..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ff0ae7d50dec8afd13f0c22741c4925e.msa +++ /dev/null @@ -1,660 +0,0 @@ ->syndip_1_chr20:63693225-63693984 -tcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactgg -taaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagt -cctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccct -atgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccaccttc -accaccaccacctccaccaccacctccaccacctccacctccaccacctccaccacctcc -accaccaccacctccaccaccaccacctccaccaccaccaccaccaccacctccaccacc -accaccaccaccaccacctccacctccaccacctccaccaccacctccacctccaccacc -acctccacctccacctccaccaccaccacctccaccacctccaccacctccacctccacc -accacctccacctccaccaccacctccacctccacctccacctccacctccaccaccacc -acctccaccacctccaccacctccacctccaccaccaccacctccacctccacctccacc -acctccacctccaccacctccacctccaccacctccaccaccaccaccaccaccaccacc -acctccaccaccaccaccaccaccacctccaccacctccacctccaccacctccaccacc -accacctccaccaccacctccaccaccacctccacctccaccacctccacctccaccacc -tccacctccacctccaccaccacctccaccacctccaccaccacctccaccacctccacc -tccaccaccaccacctccaccaccaccaccaccaccacctccaccacctccacctccacc -acctccaccaccaccacctccaccaccacctccaccaccacctccacctccaccacctcc -acctccaccacctccacctccacctccaccaccacctccaccacctccaccaccacctcc -accacctccaccacctccaccaccacctccaccacctccacctccaccaccaccacctcc -acctccaccaccaccacctccaccaccacctccacctccaccaccaccacctccacctcc -accaccaccacctccaccaccacctccaccaccaccaccaccaccaccacctccacctcc -accacctccaccaccaccaccaccacctccacctccaccacctccaccacctccaccacc -accaccaccacctccaccacctccaccaccacctccaccacctccacctccaccaccacc -acctccaccaccaccacctccacctccacctccacctccacctccaccaccacctccacc -tccaccaccacctccaccaccacctccacctccaccacctccacctccacctccaccacc -tccaccaccaccaccaccaccaccaccaccaccaccacctccaccacctccacctccacc -tccaccaccaccaccaccacctccaccaccaccaccaccacctccaccacctccaccacc -acctccaccaccaccaccaccaccaccaccaccacctccaccacctccacctccacctcc -acctccaccacctccaccacctccaccaccacctccaccaccaccaccaccacctccacc -accacctccacctccaccaccacctccaccaccacctccacctccaccacctccacctcc -accacctccaccacctccacctccaccacctccacctccacctccaccacctccaccacc -accaccaccaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctcc -accacctccaccaccacctccaccaccaccaccaccaccaccaccaccaccaccacctcc -accaccacctccacctccaccaccacctccaccaccacctccacctccaccacctccacc -tccaccacctccaccacctccaccaccaccaccaccacctccaccaccacctccacctcc -accaccaccaccaccaccaccacctccaccaccaccacctccaccaccacctccaccacc -tccaccaccacctccacctccaccacctccaccaccacctccaccaccacctccaccacc -accacctccaccaccacctccaccacctccaccaccacctccacctccaccacctccacc -accacctccaccaccacctccaccaccaccacctccaccaccacctccaccacctccacc -accacctccacctccaccacctccacctccacctccaccacctccaccaccaccaccacc -accaccaccaccaccaccaccaccaccaccaccacctccacctccacctccaccacctcc -acctccaccacctccaccaccacctccacctccaccacctccacctccacctccaccacc -tccacctccaccacctccacctccacctccaccacctccaccaccaccacctccaccacc -acctccaccacctccaccaccacctccacctccaccacctccaccaccacctccaccacc -acctccaccaccaccacctccaccaccacctccaccacctccaccaccacctccacctcc -accacctccacctccacctccaccacctccaccaccaccaccaccaccaccaccaccacc -accacctccaccaccaccacctccaccaccacctccaccaccaccaccaccacctccacc -accaccaccaccacctccaccaccacctccaccacctccaccaccaccaccaccaccacc -accacctccaccaccacctccaccaccaccaccaccaccaccaccacctccaccacctcc -acctccaccaccaccaccacctccaccaccaccaccaccaccacctccacctccaccacc -accacctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccacc -accaccacctccaccacctccaccacctccaccaccacctccaccacctccaccaccacc -accaccacctccaccaccacctccaccaccaccaccaccaccaccacctccacctccacc -tccaccacctccacctccaccacctccacctccaccacctccacctccacctccaccacc -tccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccaccacc -tccaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacctcc -accaccaccacctccaccacctccaccaccacctccaccacctccacctccaccaccacc -acctccaccaccaccacctccacctccaccaccaccaccaccaccacctccacctccacc -accacctccaccaccacctccacctccacctccaccacctccaccaccacctccaccacc -tccaccacctccacctccaccaccaccaccacctccaccaccaccaccaccacctctacc -acctctaccaccaccaccaccacctccaccaccaccaccaccacctccaccaccaccacc -accaccacctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacc -tccacctccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccacc -acctccaccaccaccaccacctccaccaccacctccaccaccacctccaccacctccacc -accaccaccacctccacctccaccacctccaccaccacctccaccaccaccaccaccacc -acctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctccacc -tccaccaccaccaccacctccacctccaccaccaccaccaccaccaccaccaccaccacc -tccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccacc -acctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccaccacc -acctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccaccaccacc -tccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccacctccacc -acctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccaccacc -acctccaccaccaccaccaccaccaccacctccaccaccacctccaccaccacctccacc -acctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccaccacc -acctccaccaccacctccaccaccaccaccaccaccacctccaccaccacctccaccacc -tccaccaccaccaccaccacctctaccacctctaccaccaccaccaccacctccaccacc -accaccacctccaccaccaccaccacctccaccaccaccacctccacctccaccaccacc -acctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacc -tccaccacctccaccaccaccaccaccaccaccaccacctccaccaccaccaccaccacc -acctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctctacc -accaccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccaccacc -acctccaccaccaccacctccacctccaccaccaccacctccaccaccaccacctccacc -tccaccaccaccacctccaccacctccaccaccacctccaccaccaccacctccacctcc -accaccaccacctccaccacctccaccaccaccacctccaccaccaccacctccaccacc -tccaccaccaccaccaccacctccaccacctccaccacctccaccaccaccaccaccacc -tccacctccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccacc -accacctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccacc -accaccaccacctccacctccacctccaccacctccaccaccaccacctccaccaccacc -acctccacctccaccacctccaccaccacctccaccaccaccacctccacctccaccacc -accacctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccacc -acctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccacc -acctccaccaccaccacctccaccacctccaccaccaccaccaccacctccaccacctcc -accacctccaccaccaccaccaccacctccacctccacctccaccacctccaccaccacc -acctccaccaccaccaccaccaccacctccaccacctccaccaccaccaccaccacctcc -acctccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccacc -accacctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccacc -tccaccaccacctccacctccacctccaccacctccacctccaccaccaccaccaccacc -accaccaccaccaccacctccacctccacctccaccaccaccacctctaccaccacctcc -accaccaccaccaccaccaccaccaccacctccaccacctccaccaccaccacctccacc -accaccacctccacctccaccaccaccaccacctccaccacctccaccaccacctccacc -tccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccacctcc -accacctccaccaccaccacctccaccaccaccacctccacctccaccacctccaccacc -tccaccaccaccaccacctccaccaccaccaccaccaccacctccacctccaccacctct -accaccacctccaccaccaccaccaccaccacctccacctccaccacctccacctccacc -acctctaccaccacctccaccaccaccacctccacctccacctccaccaccaccacctcc -acctccacctccaccaccaccaccaccaccaccacctccaccaccaccaccaccaccacc -accaccacctccacctccaccaccaccacctccaccaccaccacctccaccacctccacc -accacctccacctccaccaccaccacctccacctccacctccaccaccaccaccaccacc -tccaccaccaccacctccaccaccaacacctccacctccacctccaccaccaccaccacc -acctccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacctcc -accaccacctccaccacctccaccaccaccacctccaccaccacctccaccaccaccacc -accaccacctccacctccacctccaccaccaccacctctaccaccacctccaccaccacc -accaccaccaccaccaccacctccacctccacctccaccacctccacctccaccaccacc -accaccaccaccacctccaccaccacctccacctccacctccaccacctccacctccacc -accaccaccaccaccaccaccaccaccaccacctccacctccacctccaccaccaccacc -tctaccaccacctccaccaccaccaccaccaccaccaccaccacctccaccaccaccacc -tccacctccaccaccaccacctccacctccaccaccaccacctccacctccaccaccacc -accaccaccaccacctccaccaccaccacctccaccacctccaccaccacctccaccacc -accacctccaccacctccaccaccacctccacctccaccaccaccacctccaccaccacc -acctccacctccaccaccaccacctccacctccacctccaccacctccacctccaccacc -tccaccaccaccacctccaccacctccaccaccacctccacctccaccaccaccacctcc -accaccaccacctccaccacctccaccaccacctccacctccaccaccaccacctccacc -tccacctccaccaccaccaccaccacctccactaccaccacctccacctccaccaccacc -acctccaccaccaacacctccacctccacctccacctccaccaccaccacctccacctcc -accaccaccacctccaccaccaccacctccaccacctccacctccaccaccaccacctcc -accaccacctccaccaccaccaccacctccaccaccaccacctccaccaccacctccacc -accaccacctccaccaccacctccaccaccacctccacctccaccaccaccacctgcacc -accacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttgt -tggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccctaa -gcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtca -actgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctctgtt -tggggtggagtccaagtct ->syndip_2_chr20:63693225-63693984 -tcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactgg -taaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagt -cctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccct -atgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacca-- --------------------------------cctccacctccaccacct----------- 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-----------------------------ccacctccaccaccacctccaccacctccacc -accacctccacctccaccacctccacctccacctccaccacctccaccaccacctccacc -acctccaccacctccaccaccaccacca------------------------------cc -acctccaccacctccaccaccacctccaccacctccacctccacctccacct-------- -----------ccacctccaccaccacctccaccacct---ccaccaccacctccaccacc -acctccaccacctccacctccacctccacct----------------------------- --------------ccacctccaccaccacctccaccacctccaccaccacctccacctcc -accacctccacctccacctccaccacctccaccaccacctccaccacctccaccaccacc -tccacct----------------------------------------------------- --------ccaccacctccaccaccacctccaccacctccaccacctccaccaccaccacc -accacct----------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------ccaccacctccaccaccacctccaccacctccacctccacctccacc -t---------------------------------ccacctccaccaccacctccaccacc 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------------------------------------------------------------- --------------ccaccacctccaccaccacctccaccacctccacctccacctccacc -t---------------------------------ccacctccaccaccacctccaccacc -tccaccaccacctccacctccaccacctccacctccacctccaccacctccaccaccacc -acctccaccaccacctccaccaccaccacctccacctccaccaccacctccaccacctc- ------------------------------------------------------------- ------------------------------------------------------------- ---------------------------------caccacctccaccaccacctccaccacc -tccaccacctccaccaccaccacc---------------------------------acc -acctccaccacctccaccaccacctccaccaccaccacctccacctccacctccaccacc -tccaccacctccaccaccacctccaccacctccaccacctccaccaccacctccaccacc -tcca-------------------------------------------------------- ------------------------------------------------------------- -----------------------------ccacctccacctccaccaccaccacctccacc -acctccaccaccacctccaccacct----------------------------------- ------------------------------------------------------------- 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-accaccaccacctccacctccaccacctccaccaccacctccaccaccaccaccaccacc -acctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctccacc -tccaccaccaccaccacctccacctccaccaccaccaccaccaccaccaccaccaccacc -tccaccaccaccaccaccaccacctctaccaccaccaccaccacctccaccaccaccacc -acctccaccaccaccaccacctccaccaccacctccaccaccaccaccaccaccaccacc -acctctaccaccaccaccaccacctccaccaccaccaccacctccaccaccaccaccacc -tccaccaccacctccaccaccaccaccacctccaccaccacctccaccaccacctccacc -acctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccaccacc -acctccaccaccaccaccaccaccaccacctccaccaccacctccaccaccacctccacc -acctccaccaccaccaccaccacctccaccaccacctccacctccaccaccaccaccacc -acctccaccaccacctccaccaccaccaccaccaccacctccaccaccacctccaccacc -tccaccaccaccaccaccacctctaccacctctaccaccaccaccaccacctccaccacc -accaccacctccaccaccaccaccacctccaccaccaccacctccacctccaccaccacc -acctccaccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacc -tccaccacctccaccaccaccaccaccaccaccaccacctccaccaccaccaccaccacc -acctccaccaccacctccaccacctccaccaccaccaccaccacctctaccacctctacc -accaccaccaccacctccaccaccaccaccacctccaccaccaccaccacctccaccacc -acctccaccaccaccacctccacctccaccaccaccacctccaccaccaccacctccacc -tccaccaccaccacctccaccacctccaccaccacctccaccaccaccacctccacctcc -accaccaccacctccaccacctccaccaccaccacctccaccaccaccacctccaccacc -tccaccaccaccaccaccacctccaccacctccaccacctccaccaccaccaccaccacc -tccacctccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccacc -accacctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccacc -accaccaccacctccacctccacctccaccacctccaccaccaccacctccaccaccacc -acctccacctccaccacctccaccaccacctccaccaccaccacctccacctccaccacc -accacctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccacc -acctccaccaccaccacctccacctccaccaccaccacctccaccacctccaccaccacc -acctccaccaccaccacctccaccacctccaccaccaccaccaccacctccaccacctcc -accacctccaccaccaccaccaccacctccacctccacctccaccacctccaccaccacc -acctccaccaccaccaccaccaccacctccaccacctccaccaccaccaccaccacctcc -acctccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccacc -accacctccacctccacctccaccacctccacctccaccaccaccaccaccaccaccacc -tccaccaccacctccacctccacctccaccacctccacctccaccaccaccaccaccacc -accaccaccaccaccacctccacctccacctccaccaccaccacctctaccaccacctcc -accaccaccaccaccaccaccaccaccacctccaccacctccaccaccaccacctccacc -accaccacctccacctccaccaccaccaccacctccaccacctccaccaccacctccacc -tccacctccaccacctccaccaccaccacctccaccaccaccaccaccaccaccacctcc -accacctccaccaccaccacctccaccaccaccacctccacctccaccacctccaccacc -tccaccaccaccaccacctccaccaccaccaccaccaccacctccacctccaccacctct -accaccacctccaccaccaccaccaccaccacctccacctccaccacctccacctccacc -acctctaccaccacctccaccaccaccacctccacctccacctccaccaccaccacctcc -acctccacctccaccaccaccaccaccaccaccacctccaccaccaccaccaccaccacc -accaccacctccacctccaccaccaccacctccaccaccaccacctccaccacctccacc -accacctccacctccaccaccaccacctccacctccacctccaccaccaccaccaccacc -tccaccaccaccacctccaccaccaacacctccacctccacctccaccaccaccaccacc -acctccacctccaccaccacctccaccaccaccacctccacctccaccaccaccacctcc -accaccacctccaccacctccaccaccaccacctccaccaccacctccaccaccaccacc -accaccacctccacctccacctccaccaccaccacctctaccaccacctccaccaccacc -accaccaccaccaccaccacctccacctccacctccaccacctccacctccaccaccacc -accaccaccaccacctccaccaccacctccacctccacctccaccacctccacctccacc -accaccaccaccaccaccaccaccaccaccacctccacctccacctccaccaccaccacc -tctaccaccacctccaccaccaccaccaccaccaccaccaccacctccaccaccaccacc -tccacctccaccaccaccacctccacctccaccaccaccacctccacctccaccaccacc -accaccaccaccacctccaccaccaccacctccaccacctccaccaccacctccaccacc -accacctccaccacctccaccaccacctccacctccaccaccaccacctccaccaccacc -acctccacctccaccaccaccacctccacctccacctccaccacctccacctccaccacc -tccaccaccaccacctccaccacctccaccaccacctccacctccaccaccaccacctcc -accaccaccacctccaccacctccaccaccacctccacctccaccaccaccacctccacc -tccacctccaccaccaccaccaccacctccactaccaccacctccacctccaccaccacc -acctccaccaccaacacctccacctccacctccacctccaccaccaccacctccacctcc -accaccaccacctccaccaccaccacctccaccacctccacctccaccaccaccacctcc -accaccacctccaccaccaccaccacctccaccaccaccacctccaccaccacctccacc -accaccacctccaccaccacctccaccaccacctccacctccaccaccaccacctgcacc -accacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttgt -tggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccctaa -gcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtca -actgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctctgtt -tggggtggagtccaagtct ->ref_chr20:63693225-63693984 -tcggcctgagcacagcattccccgaaggcagcgggcacagccggtcctggaccccactgg -taaatggggccccaggtgggaccctcagactcctgcgtggaaggcagtgtgggccagagt -cctgggctgcttggggtgggcatcctcgggccctgcttggccccgcctctctgttcccct -atgggagtgatgggggcctccacctccaccaccagcaccagcagcaccacctccacct-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------ccacctccacct----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------------ccacc -tccaccaccacctccacctccaccaccacctcctccaccaccaccacctccaccaccacc -accaccaccaccacctccacctccaccacctccacctccaccaccaccacctccacct-- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------ccaccaccacc -acctccacctccaccaccacctccaccaccaccacctccacctccacca----------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------------------------------ccacctccacc -accaccaccaccaccaccaccaccaccacca----------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- -----------------------------------ccacctccaccaccaccacctgcacc -accacctccacctccaccaccaccaccacctccacctccaccagcagcagcatcacttgt -tggggagaccctgtgcaactccatgcacagccctgtccctgccatagccccgacccctaa -gcacagccctgtccaactgccacacgtcccctgcctcccatgcatggtcctggggggtca -actgcacacgccagggtcctagggtcctagacccctgtcctccctgtttctgcctctgtt -tggggtggagtccaagtct diff --git a/repo_utils/test_files/external/fake_mafft/lookup/fm_ff5bbed9fc29f7f0637d3929908a94a3.msa b/repo_utils/test_files/external/fake_mafft/lookup/fm_ff5bbed9fc29f7f0637d3929908a94a3.msa deleted file mode 100644 index 25f289a0..00000000 --- a/repo_utils/test_files/external/fake_mafft/lookup/fm_ff5bbed9fc29f7f0637d3929908a94a3.msa +++ /dev/null @@ -1,80 +0,0 @@ ->syndip_1_chr20:63641679-63642235 -tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc -tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct -cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca -gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag -ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgccccc -cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc -tccgagctccgccccgg------------------------------------------- ------------------------------------------------------------- -------------------------------ccccgccccggcccctgcccgctccgagct -ccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccccc -gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc -gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc -ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc -gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt ->syndip_2_chr20:63641679-63642235 -tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc -tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct -cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca -gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag -ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc -cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc -tccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgcc -ctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccagt -gccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagct -ccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc -tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc -gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc -ccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagcc -gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt ->p:HG002_1_chr20:63641679-63642235 -tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc -tgctggggacgcccagtaaacacgggaggagcccccgatccccaccccagctcagcgcct -cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca -gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag -ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc -cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc -tccgagctccaccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgcc -ctgccccctccccggcccctgcccgctccgagctccgccccggccccgccccggcccagt -gccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgagct -ccgccctggccccgcccccgcccagtgccccgccccctgcctgctgcttgccctgccccc -tccccggcccctgcccgctccgagctccgccccggcctcgccccggcccctgcccgctcc -gagcttcgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc -ccggcccctgcccgctccgaactccgccccggccccgcccccgcaccttctcgcgcagcc -gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt ->p:HG002_2_chr20:63641679-63642235 -tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc -tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct -cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca -gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag -ctccgccctggccccgccccggcccctgcccgctccgagctccgccctggccccgccccc -cgcccagtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgc -tccgagctccgccccgg------------------------------------------- ------------------------------------------------------------- -------------------------------ccccgccccggcccctgcccgctccgagct -ccgccctggccccgcccccgcccagtgccccgccccctgactgctgctagccctgccccc -gccccggcccctgcccgctccgagctccgccccggccccgccccggcccctgcccgctcc -gagctccgccccggccccgccccggcccctgcccgctccgagcttcgccccggccccgcc -ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc -gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt ->ref_chr20:63641679-63642235 -tctattactgcggctagttactgtcccgccaggaccagactctggacctgcctcgtgcgc -tgctggggacgcccagtaaacacgggaggagcccccgacccccaccccagctcagcgcct -cggagtccccggccccgctctgcgcccctccgagctccgccctagccccgcccccgccca -gtgccccgccccctgcctgctgctagccctgcccccgccccggcccctgcccgctccgag -ctccgccccggccccgccccggcccctgcccgctccgagctccgccctggccccg-cccc -cgcccagtgccccgccccctgactgctgctagccctgc---------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ---------------ccccgccccggcccctgcccgctccgagcttcgccccggccccgcc -ccggcccctgcccgctccgagctccgccccggccccgcccccgcaccttctcgcgcagcc -gctcgcgcagtgcggccaggtgtgcctcgcggatctccttgctgagctccatcttgtagt -tgagcttctcctccgcctggcggctgaagttgttattctcctccagcgccttgt diff --git a/truvari/__init__.py b/truvari/__init__.py index 77121047..6c6c9f9b 100644 --- a/truvari/__init__.py +++ b/truvari/__init__.py @@ -67,7 +67,7 @@ :data:`truvari.SZBINTYPE` """ -__version__ = '5.1.1' +__version__ = '5.2.0' from truvari.bench import ( diff --git a/truvari/bench.py b/truvari/bench.py index 826cdc3b..1dc36ac3 100644 --- a/truvari/bench.py +++ b/truvari/bench.py @@ -650,56 +650,65 @@ def pick_ac_matches(match_matrix): match_matrix = np.ravel(match_matrix) match_matrix.sort() used_comp = Counter() + written_comp = defaultdict(bool) used_base = Counter() + written_base = defaultdict(bool) + + # Make a pass for TPs only for match in match_matrix[::-1]: - # No more matches to find - if base_cnt == 0 and comp_cnt == 0: - break + if not match.state: + continue + b_key = str(match.base) c_key = str(match.comp) - # This is a trick + base_is_used = used_base[b_key] >= match.base_gt_count comp_is_used = used_comp[c_key] >= match.comp_gt_count - # Only write the comp (FP) - if base_cnt == 0 and not comp_is_used: + if base_is_used or comp_is_used: + match.state = False + match.multi = True + continue + + # How often this variant has been used is updated + used_comp[c_key] += match.base_gt_count + used_base[b_key] += match.comp_gt_count + + # Only write once + if not written_comp[c_key]: + written_comp[c_key] = True to_process = copy.copy(match) to_process.base = None - to_process.multi = to_process.state - to_process.state = False - comp_cnt -= 1 - if used_comp[c_key] == 0: # Only write as F if it hasn't been a T - ret.append(to_process) - used_comp[c_key] = 9 - # Only write the base (FN) - elif comp_cnt == 0 and not base_is_used: + ret.append(to_process) + if not written_base[b_key]: + written_base[b_key] = True to_process = copy.copy(match) to_process.comp = None - to_process.multi = to_process.state - to_process.state = False - base_cnt -= 1 - if used_base[b_key] == 0: # Only write as F if it hasn't been a T - ret.append(to_process) - used_base[b_key] = 9 - # Write both (any state) - elif not base_is_used and not comp_is_used: + ret.append(to_process) + + # Make a pass for all remaining FP/FNs + for match in match_matrix[::-1]: + if match.state: + continue + + b_key = str(match.base) + c_key = str(match.comp) + + # Only write once + if not written_comp[c_key]: + written_comp[c_key] = True + to_process = copy.copy(match) + to_process.base = None + ret.append(to_process) + + if not written_base[b_key]: + written_base[b_key] = True to_process = copy.copy(match) - # Don't write twice - if used_base[b_key] != 0: - to_process.base = None - if used_comp[c_key] != 0: - to_process.comp = None - - used_base[b_key] += match.comp_gt_count - used_comp[c_key] += match.base_gt_count - # All used up - if used_base[b_key] >= match.base_gt_count: - base_cnt -= 1 - if used_comp[c_key] >= match.comp_gt_count: - comp_cnt -= 1 - - # Safety edge case check - if to_process.base is not None or to_process.comp is not None: - ret.append(to_process) + to_process.comp = None + ret.append(to_process) + + if len(written_comp) >= comp_cnt and len(written_base) >= base_cnt: + break + return ret diff --git a/truvari/make_ga4gh.py b/truvari/make_ga4gh.py index 7f2f873c..3743cae9 100644 --- a/truvari/make_ga4gh.py +++ b/truvari/make_ga4gh.py @@ -315,4 +315,6 @@ def make_ga4gh_main(args): pull_refine=args.no_refine, write_phab=args.write_phab) logging.info("Stats: %s", json.dumps(output.stats, indent=4)) + with open(args.output + '.summary.json' ,'w') as fout: + json.dump(output.stats, fout, indent=4) logging.info("Finished") diff --git a/truvari/msatovcf.py b/truvari/msatovcf.py index 17047dc0..c78ed6db 100644 --- a/truvari/msatovcf.py +++ b/truvari/msatovcf.py @@ -140,7 +140,7 @@ def msa2vcf(msa, anchor_base='N'): >>> import truvari >>> from truvari.phab import fasta_reader >>> msa_dir = "repo_utils/test_files/external/fake_mafft/lookup/" - >>> msa_file = "fm_0c8572a4abbd43dfe7727d1bbe104e58.msa" + >>> msa_file = "fm_03ffe346bf2196b0ceebee5beb9a6acb.msa" >>> seqs = open(msa_dir + msa_file).read() >>> fasta = dict(fasta_reader(seqs)) >>> m_entries_str = truvari.msa2vcf(fasta) diff --git a/truvari/phab.py b/truvari/phab.py index ef2fd586..aeac72fd 100644 --- a/truvari/phab.py +++ b/truvari/phab.py @@ -407,8 +407,8 @@ def parse_args(args): help="Output VCF") parser.add_argument("--buffer", type=int, default=100, help="Number of reference bases before/after region to add to MSA (%(default)s)") - parser.add_argument("--align", type=str, choices=["mafft", "wfa", "poa"], default="mafft", - help="Alignment method accurate (mafft), fast (wfa), medium (poa) (%(default)s)") + parser.add_argument("--align", type=str, choices=["mafft", "wfa", "poa"], default="poa", + help="Alignment method (%(default)s)") parser.add_argument("-m", "--mafft-params", type=str, default=DEFAULT_MAFFT_PARAM, help="Parameters for mafft, wrap in a single quote (%(default)s)") parser.add_argument("--bSamples", type=str, default=None, diff --git a/truvari/refine.py b/truvari/refine.py index 72dc441e..93df51d2 100644 --- a/truvari/refine.py +++ b/truvari/refine.py @@ -241,7 +241,7 @@ def parse_args(args): formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument("benchdir", metavar="DIR", help="Truvari bench directory") - parser.add_argument("-a", "--align", type=str, choices=["mafft", "wfa", "poa"], default="mafft", + parser.add_argument("-a", "--align", type=str, choices=["mafft", "wfa", "poa"], default="poa", help="Alignment method for phab (%(default)s)") parser.add_argument("-u", "--use-original-vcfs", action="store_true", help="Use original input VCFs instead of filtered tp/fn/fps") @@ -296,7 +296,7 @@ def check_params(args): elif args.reference is None: args.reference = params["reference"] - if not os.path.exists(args.reference): + if args.reference is not None and not os.path.exists(args.reference): check_fail = True logging.error("Reference %s does not exist", args.reference) diff --git a/truvari/region_vcf_iter.py b/truvari/region_vcf_iter.py index 6676932c..844b911a 100644 --- a/truvari/region_vcf_iter.py +++ b/truvari/region_vcf_iter.py @@ -211,6 +211,7 @@ def region_filter_fetch(vcf, tree, with_region=False): chrom, vcf.filename) +# pylint: disable=too-many-statements def region_filter_stream(vcf, tree, inside=True, with_region=False): """ Given a VariantRecord iter and defaultdict(IntervalTree), diff --git a/truvari/variant_record.py b/truvari/variant_record.py index d311d726..0c949fdc 100644 --- a/truvari/variant_record.py +++ b/truvari/variant_record.py @@ -690,7 +690,7 @@ def resolve(self, ref): return True - def same_type(self, other, dup_to_ins=False): + def same_type(self, other): """ Check if self.var_type() == other.var_type() with extra handling for dup-to-ins @@ -704,13 +704,13 @@ def same_type(self, other, dup_to_ins=False): """ a_type = self.var_type() b_type = other.var_type() - if dup_to_ins and a_type == truvari.SV.DUP: + if self.params.dup_to_ins and a_type == truvari.SV.DUP: a_type = truvari.SV.INS - if dup_to_ins and b_type == truvari.SV.DUP: + if self.params.dup_to_ins and b_type == truvari.SV.DUP: b_type = truvari.SV.INS return a_type == b_type - def seqsim(self, other, roll=True): + def seqsim(self, other): """ Calculate sequence similarity of two entries. If reference is not None, compare their shared reference context. Otherwise, use the unroll technique. @@ -741,7 +741,7 @@ def seqsim(self, other, roll=True): b_seq = b_seq.upper() st_dist, ed_dist = self.distance(other) - if not roll or st_dist == 0 or ed_dist == 0: + if not self.params.no_roll or st_dist == 0 or ed_dist == 0: return truvari.seqsim(a_seq, b_seq) # Return best of rolled, unrolled from both ends, and direct similarity