Moving to poa default

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

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

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}
+{"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}

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
         }
     }
 }

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

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
@@ -201,25 +201,25 @@ 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
 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

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
 }