fixing refine

default `--coords` wasn't set right

repo_utils/answer_key/refine/refine_output_three/phab_bench/candidate.refine.bed

@@ -1,21 +1,30 @@
 chr20	2240950	2241281
-chr20	4032347	4033215
-chr20	5041931	5042278
-chr20	8661921	8662129
-chr20	14862045	14862654
-chr20	18209129	18210126
-chr20	20354902	20355445
-chr20	20356520	20357806
-chr20	22082256	22083915
+chr20	4032347	4033346
+chr20	14861956	14862620
+chr20	16257844	16259215
+chr20	18209129	18210249
+chr20	20354902	20357861
+chr20	21721596	21721710
+chr20	22082256	22083544
 chr20	23155541	23155867
-chr20	38123851	38124009
-chr20	55944262	55945185
-chr20	56280531	56281923
-chr20	57948991	57949344
-chr20	62057653	62058902
-chr20	62270590	62270817
-chr20	62349631	62349830
-chr20	62360425	62360610
-chr20	63948617	63948698
-chr20	64131999	64133807
-chr20	64173428	64176340
+chr20	35580680	35580870
+chr20	38123851	38124122
+chr20	50775888	50775909
+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	63154677	63154931
+chr20	63693446	63693676
+chr20	63948617	63948750
+chr20	64131937	64133833
+chr20	64173531	64176450

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/v2zu1oew.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}
+{"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}

repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json

@@ -1,30 +1,31 @@
 {
-    "TP-base": 150,
-    "TP-comp": 150,
-    "FP": 25,
-    "FN": 44,
-    "precision": 0.8571428571428571,
-    "recall": 0.7731958762886598,
-    "f1": 0.8130081300813008,
-    "base cnt": 194,
-    "comp cnt": 175,
-    "TP-comp_TP-gt": 143,
-    "TP-comp_FP-gt": 7,
-    "TP-base_TP-gt": 143,
-    "TP-base_FP-gt": 7,
-    "gt_concordance": 0.9533333333333334,
+    "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,
     "gt_matrix": {
-        "(1, 1)": {
-            "(0, 1)": 4,
-            "(1, 0)": 3,
-            "(1, 1)": 14
+        "(1, 0)": {
+            "(0, 1)": 105
         },
         "(0, 1)": {
-            "(1, 0)": 50,
-            "(0, 1)": 1
+            "(1, 0)": 86,
+            "(1, 1)": 2,
+            "(0, 1)": 4
         },
-        "(1, 0)": {
-            "(0, 1)": 78
+        "(1, 1)": {
+            "(0, 1)": 7,
+            "(1, 1)": 21,
+            "(1, 0)": 2
         }
     }
 }

repo_utils/answer_key/refine/refine_output_three/refine.region_summary.json

@@ -1,18 +1,18 @@
 {
-    "TP": 149,
-    "TN": 45,
+    "TP": 40,
+    "TN": 1,
     "FP": 27,
-    "FN": 18,
-    "base P": 170,
-    "base N": 54,
-    "comp P": 178,
-    "comp N": 46,
-    "PPV": 0.8370786516853933,
-    "TPR": 0.8764705882352941,
-    "TNR": 0.8333333333333334,
-    "NPV": 0.9782608695652174,
-    "ACC": 0.8660714285714286,
-    "BA": 0.8549019607843138,
-    "F1": 0.8563218390804598,
+    "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,
+    "ACC": 0.5,
+    "BA": 0.3277777777777778,
+    "F1": 0.5263157894736842,
     "UND": 0
 }