Merge branch 'feature/gtcolap' into develop

.pylintrc

@@ -51,7 +51,7 @@ enable=all
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-disable=unsupported-assignment-operation,locally-disabled,locally-enalbed,suppressed-message,fixme,cyclic-import,duplicate-code,invalid-name,too-many-nested-blocks,too-many-branches,no-member,logging-fstring-interpolation,edlib,unspecified-encoding,bad-option-value
+disable=unsupported-assignment-operation,locally-disabled,locally-enalbed,suppressed-message,fixme,cyclic-import,duplicate-code,invalid-name,too-many-nested-blocks,too-many-branches,no-member,logging-fstring-interpolation,edlib,unspecified-encoding,bad-option-value,use-implicit-booleaness-not-comparison-to-zero
 
 
 [REPORTS]

repo_utils/answer_key/bench/bench_unroll/candidate.refine.bed

@@ -0,0 +1,30 @@
+chr21	14088107	14089536
+chr21	14256930	14256968
+chr21	14439479	14439480
+chr21	14667323	14667354
+chr21	14671569	14671603
+chr21	14891950	14891951
+chr21	15030990	15031103
+chr21	15089462	15089463
+chr21	15556506	15556507
+chr21	16187358	16187359
+chr21	16359640	16359950
+chr21	16730887	16731579
+chr21	16925119	16925171
+chr21	16972598	16972913
+chr21	17240010	17241315
+chr21	17292195	17292196
+chr21	17400105	17400106
+chr21	17432393	17432433
+chr21	17501572	17501626
+chr21	17696939	17696940
+chr21	17719505	17720505
+chr21	17730246	17730247
+chr21	17903115	17903116
+chr21	18144978	18144979
+chr21	18436845	18436879
+chr21	18587125	18587176
+chr21	18859198	18859269
+chr21	19170599	19170633
+chr21	19313754	19313790
+chr21	20288211	20288212

repo_utils/answer_key/bench/bench_unroll/log.txt

@@ -1,48 +1,47 @@
-2022-12-01 18:26:06,498 [INFO] Truvari v4.0.0.dev0+detached
-2022-12-01 18:26:06,499 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/real_small_base.vcf.gz -c repo_utils/test_files/variants/real_small_comp.vcf.gz -o test_results/bench_unroll/
-2022-12-01 18:26:06,500 [INFO] Params:
+2023-11-01 14:02:05,211 [INFO] Truvari v4.1.1.dev0+a08d9a7.uc
+2023-11-01 14:02:05,212 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/real_small_base.vcf.gz -c repo_utils/test_files/variants/real_small_comp.vcf.gz -o test_results/bench_unroll/
+2023-11-01 14:02:05,214 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/real_small_base.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/real_small_comp.vcf.gz",
     "output": "test_results/bench_unroll/",
-    "reference": null,
+    "includebed": null,
+    "extend": 0,
     "debug": false,
-    "prog": false,
+    "reference": null,
     "refdist": 500,
-    "pctsim": 0.7,
+    "pctseq": 0.7,
     "minhaplen": 50,
     "pctsize": 0.7,
     "pctovl": 0.0,
     "typeignore": false,
-    "dup_to_ins": false,
-    "use_lev": false,
     "chunksize": 1000,
-    "gtcomp": false,
     "bSample": "NA12878",
     "cSample": "NULL",
+    "dup_to_ins": false,
     "sizemin": 50,
     "sizefilt": 30,
     "sizemax": 50000,
     "passonly": false,
     "no_ref": false,
-    "includebed": null,
-    "extend": 0,
-    "multimatch": false
+    "pick": "single",
+    "check_monref": true,
+    "check_multi": true
 }
-2022-12-01 18:26:06,562 [INFO] Zipped 71 variants Counter({'base': 43, 'comp': 28})
-2022-12-01 18:26:06,563 [INFO] 45 chunks of 71 variants Counter({'base': 43, 'comp': 28})
-2022-12-01 18:26:06,567 [INFO] Stats: {
+2023-11-01 14:02:05,282 [INFO] Zipped 71 variants Counter({'base': 43, 'comp': 28})
+2023-11-01 14:02:05,283 [INFO] 45 chunks of 71 variants Counter({'base': 43, 'comp': 28})
+2023-11-01 14:02:05,396 [INFO] Stats: {
     "TP-base": 18,
-    "TP-call": 18,
+    "TP-comp": 18,
     "FP": 1,
     "FN": 25,
     "precision": 0.9473684210526315,
     "recall": 0.4186046511627907,
     "f1": 0.5806451612903226,
     "base cnt": 43,
-    "call cnt": 19,
-    "TP-call_TP-gt": 0,
-    "TP-call_FP-gt": 18,
+    "comp cnt": 19,
+    "TP-comp_TP-gt": 0,
+    "TP-comp_FP-gt": 18,
     "TP-base_TP-gt": 0,
     "TP-base_FP-gt": 18,
     "gt_concordance": 0.0,
@@ -56,6 +55,26 @@
         "(1, 1)": {
             "(None, None)": 6
         }
+    },
+    "weighted": {
+        "sequence": {
+            "TP": 18.180799916386604,
+            "FP": 2.3630000948905945,
+            "FN": 24.819200083613396,
+            "precision": 0.8849774582310252,
+            "recall": 0.42280930038108383,
+            "f1": 0.572228916531905,
+            "total": 44
+        },
+        "size": {
+            "TP": 18.139900118112564,
+            "FP": 2.1082999110221863,
+            "FN": 24.860099881887436,
+            "precision": 0.8958771689340982,
+            "recall": 0.42185814228168755,
+            "f1": 0.5736100034390409,
+            "total": 44
+        }
     }
 }
-2022-12-01 18:26:06,694 [INFO] Finished bench
+2023-11-01 14:02:05,397 [INFO] Finished bench

repo_utils/answer_key/bench/bench_unroll/params.json

@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/real_small_base.vcf.gz", "comp": "/data/repo_utils/test_files/variants/real_small_comp.vcf.gz", "output": "test_results/bench_unroll/", "reference": null, "debug": false, "prog": false, "refdist": 500, "pctsim": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "dup_to_ins": false, "use_lev": false, "chunksize": 1000, "gtcomp": false, "bSample": "NA12878", "cSample": "NULL", "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "includebed": null, "extend": 0, "multimatch": false}
+{"base": "/data/repo_utils/test_files/variants/real_small_base.vcf.gz", "comp": "/data/repo_utils/test_files/variants/real_small_comp.vcf.gz", "output": "test_results/bench_unroll/", "includebed": null, "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA12878", "cSample": "NULL", "dup_to_ins": false, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}

repo_utils/answer_key/bench/bench_unroll/summary.json

@@ -23,5 +23,25 @@
         "(1, 1)": {
             "(None, None)": 6
         }
+    },
+    "weighted": {
+        "sequence": {
+            "TP": 18.180799916386604,
+            "FP": 2.3630000948905945,
+            "FN": 24.819200083613396,
+            "precision": 0.8849774582310252,
+            "recall": 0.42280930038108383,
+            "f1": 0.572228916531905,
+            "total": 44
+        },
+        "size": {
+            "TP": 18.139900118112564,
+            "FP": 2.1082999110221863,
+            "FN": 24.860099881887436,
+            "precision": 0.8958771689340982,
+            "recall": 0.42185814228168755,
+            "f1": 0.5736100034390409,
+            "total": 44
+        }
     }
-}
+}