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Merge branch 'feature/consensus' into develop
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@ACEnglish
ACEnglish committed Dec 19, 2023
2 parents 4a49be8 + 9d9da3b commit 64b1fa7
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Showing 85 changed files with 5,131 additions and 6,007 deletions.
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16 changes: 8 additions & 8 deletions repo_utils/answer_key/refine/refine_output_one/log.txt
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2023-11-01 14:04:28,717 [INFO] Truvari v4.1.1.dev0+a08d9a7.uc
2023-11-01 14:04:28,719 [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
2023-11-01 14:04:28,720 [INFO] Params:
2023-12-19 15:33:50,086 [INFO] Truvari v4.2.0rc1
2023-12-19 15:33:50,088 [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
2023-12-19 15:33:50,089 [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",
Expand Down Expand Up @@ -28,10 +28,10 @@
"check_monref": true,
"check_multi": true
}
2023-11-01 14:04:28,793 [INFO] Including 225 bed regions
2023-11-01 14:04:30,301 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855})
2023-11-01 14:04:30,302 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451})
2023-11-01 14:04:30,471 [INFO] Stats: {
2023-12-19 15:33:50,173 [INFO] Including 225 bed regions
2023-12-19 15:33:51,903 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855})
2023-12-19 15:33:51,904 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451})
2023-12-19 15:33:52,077 [INFO] Stats: {
"TP-base": 387,
"TP-comp": 387,
"FP": 64,
Expand Down Expand Up @@ -83,4 +83,4 @@
}
}
}
2023-11-01 14:04:30,472 [INFO] Finished bench
2023-12-19 15:33:52,078 [INFO] Finished bench
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8 changes: 2 additions & 6 deletions repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed
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@@ -1,9 +1,5 @@
chr20 5040476 5040477
chr20 5041941 5042433
chr20 7720952 7720968
chr20 16257854 16259205
chr20 24682040 24682100
chr20 51953819 51953820
chr20 55627638 55628305
chr20 63028079 63029030
chr20 64134990 64135242
chr20 32723044 32723045
chr20 51953819 51953820
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2 changes: 1 addition & 1 deletion repo_utils/answer_key/refine/refine_output_one/phab_bench/params.json
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{"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/c7gxuj5a.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single", "check_monref": true, "check_multi": true}
{"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/yw_a31jd.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single", "check_monref": true, "check_multi": true}
57 changes: 28 additions & 29 deletions repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json
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@@ -1,48 +1,47 @@
{
"TP-base": 379,
"TP-comp": 379,
"FP": 7,
"FN": 3,
"precision": 0.9818652849740933,
"recall": 0.9921465968586387,
"f1": 0.9869791666666666,
"base cnt": 382,
"comp cnt": 386,
"TP-comp_TP-gt": 379,
"TP-base": 381,
"TP-comp": 381,
"FP": 4,
"FN": 2,
"precision": 0.9896103896103896,
"recall": 0.9947780678851175,
"f1": 0.9921875,
"base cnt": 383,
"comp cnt": 385,
"TP-comp_TP-gt": 381,
"TP-comp_FP-gt": 0,
"TP-base_TP-gt": 379,
"TP-base_TP-gt": 381,
"TP-base_FP-gt": 0,
"gt_concordance": 1.0,
"gt_matrix": {
"(0, 1)": {
"(1, 0)": 143
"(1, 0)": 145
},
"(1, 0)": {
"(0, 1)": 184,
"(1, 0)": 1
"(0, 1)": 184
},
"(1, 1)": {
"(1, 1)": 51
"(1, 1)": 52
}
},
"weighted": {
"sequence": {
"TP": 384.0702000260353,
"FP": 4.3610000014305115,
"FN": 0.5952999591827393,
"precision": 0.9887727865291919,
"recall": 0.9984524217555106,
"f1": 0.9935890297287107,
"total": 389
"TP": 382.03810000419617,
"FP": 3.716600000858307,
"FN": 1.2736999988555908,
"precision": 0.9903653798623592,
"recall": 0.9966771176915361,
"f1": 0.9935112243223944,
"total": 387
},
"size": {
"TP": 384.2482999712229,
"FP": 4.497000023722649,
"FN": 0.2547000050544739,
"precision": 0.9884320144223451,
"recall": 0.9993375864295723,
"f1": 0.9938548846095698,
"total": 389
"TP": 382.14099998772144,
"FP": 3.820500001311302,
"FN": 1.0385000109672546,
"precision": 0.990101344301388,
"recall": 0.9972897819142965,
"f1": 0.9936825627390087,
"total": 387
}
}
}
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34 changes: 17 additions & 17 deletions repo_utils/answer_key/refine/refine_output_one/refine.log.txt
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@@ -1,6 +1,6 @@
2023-11-01 14:04:32,128 [INFO] Truvari v4.1.1.dev0+a08d9a7.uc
2023-11-01 14:04:32,129 [INFO] Command /data/truvari/__main__.py refine -u -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_one
2023-11-01 14:04:32,131 [INFO] Params:
2023-12-19 15:33:53,701 [INFO] Truvari v4.2.0rc1
2023-12-19 15:33:53,702 [INFO] Command /data/truvari/__main__.py refine -u -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_one
2023-12-19 15:33:53,703 [INFO] Params:
{
"benchdir": "test_results/refine_output_one",
"reference": "repo_utils/test_files/refine_data/chr20.fa.gz",
Expand All @@ -13,17 +13,17 @@
"mafft_params": "--auto --thread 1",
"debug": false
}
2023-11-01 14:04:32,132 [INFO] Setting up regions
2023-11-01 14:04:32,154 [INFO] Evaluating 225 regions
2023-11-01 14:04:32,712 [INFO] 85 regions to be refined
2023-11-01 14:04:32,757 [INFO] Preparing regions
2023-11-01 14:04:32,769 [INFO] Extracting haplotypes
2023-11-01 14:05:28,548 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
2023-11-01 14:05:28,553 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
2023-11-01 14:05:28,557 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
2023-11-01 14:05:28,651 [INFO] Harmonizing variants
2023-11-01 14:05:31,650 [INFO] Running bench
2023-11-01 14:05:31,716 [INFO] Including 85 bed regions
2023-11-01 14:05:32,942 [INFO] Zipped 4154 variants Counter({'base': 2077, 'comp': 2077})
2023-11-01 14:05:32,943 [INFO] 85 chunks of 4154 variants Counter({'__filtered': 3386, 'comp': 386, 'base': 382})
2023-11-01 14:05:33,483 [INFO] Finished refine
2023-12-19 15:33:53,704 [INFO] Setting up regions
2023-12-19 15:33:53,725 [INFO] Evaluating 225 regions
2023-12-19 15:33:54,307 [INFO] 85 regions to be refined
2023-12-19 15:33:54,344 [INFO] Preparing regions
2023-12-19 15:33:54,354 [INFO] Extracting haplotypes
2023-12-19 15:33:55,039 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
2023-12-19 15:33:55,041 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
2023-12-19 15:33:55,154 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
2023-12-19 15:33:55,162 [INFO] Harmonizing variants
2023-12-19 15:33:57,833 [INFO] Running bench
2023-12-19 15:33:57,887 [INFO] Including 85 bed regions
2023-12-19 15:33:59,098 [INFO] Zipped 4106 variants Counter({'base': 2053, 'comp': 2053})
2023-12-19 15:33:59,100 [INFO] 86 chunks of 4106 variants Counter({'__filtered': 3338, 'comp': 385, 'base': 383})
2023-12-19 15:33:59,647 [INFO] Finished refine
26 changes: 13 additions & 13 deletions repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json
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@@ -1,18 +1,18 @@
{
"TP": 194,
"TN": 15,
"FP": 13,
"FN": 3,
"base P": 201,
"base N": 24,
"TP": 199,
"TN": 14,
"FP": 10,
"FN": 2,
"base P": 202,
"base N": 23,
"comp P": 210,
"comp N": 15,
"PPV": 0.9238095238095239,
"TPR": 0.9651741293532339,
"TNR": 0.625,
"NPV": 1.0,
"ACC": 0.9288888888888889,
"BA": 0.7950870646766169,
"F1": 0.9440389294403894,
"PPV": 0.9476190476190476,
"TPR": 0.9851485148514851,
"TNR": 0.6086956521739131,
"NPV": 0.9333333333333333,
"ACC": 0.9466666666666667,
"BA": 0.7969220835126991,
"F1": 0.9660194174757282,
"UND": 0
}
14 changes: 7 additions & 7 deletions repo_utils/answer_key/refine/refine_output_one/refine.regions.txt
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Expand Up @@ -19,7 +19,7 @@ chr20 5554104 5554185 0 0 0 0 False 0 0 0 0 TN
chr20 5962327 5962410 0 0 0 0 False 0 0 0 0 TN
chr20 7435215 7435749 2 2 0 0 False 2 2 0 0 TP
chr20 7719330 7719414 1 1 0 0 False 1 1 0 0 TP
chr20 7720911 7721003 1 1 1 0 True 1 1 1 0 FN
chr20 7720911 7721003 1 1 1 0 True 1 1 0 0 TP
chr20 7721059 7721319 0 0 0 0 False 0 0 0 0 TN
chr20 8661911 8662657 1 1 3 1 True 9 9 0 0 TP
chr20 9015548 9016039 1 1 0 0 False 1 1 0 0 TP
Expand Down Expand Up @@ -55,7 +55,7 @@ chr20 23267965 23268087 2 2 0 0 False 2 2 0 0 TP
chr20 23560883 23561191 1 1 2 2 True 3 3 0 0 TP
chr20 23942431 23942955 1 1 0 0 False 1 1 0 0 TP
chr20 24407983 24408997 3 3 1 0 True 2 2 0 0 TP
chr20 24681988 24682277 2 2 1 0 True 1 1 0 1 FP
chr20 24681988 24682277 2 2 1 0 True 2 2 0 0 TP
chr20 24836081 24836384 2 2 0 0 False 2 2 0 0 TP
chr20 24956961 24957198 2 2 0 0 False 2 2 0 0 TP
chr20 24982027 24982423 1 1 0 0 False 1 1 0 0 TP
Expand All @@ -66,7 +66,7 @@ chr20 29401872 29402283 0 0 0 0 False 0 0 0 0 TN
chr20 29799755 29799978 0 0 0 0 False 0 0 0 0 TN
chr20 30404513 30406201 0 0 0 0 False 0 0 0 0 TN
chr20 31689079 31689527 2 2 0 0 False 2 2 0 0 TP
chr20 32722424 32723212 0 0 1 0 True 0 0 0 0 TN
chr20 32722424 32723212 0 0 1 0 True 0 0 1 0 FN
chr20 32723469 32724637 0 0 0 0 False 0 0 0 0 TN
chr20 32724927 32724999 0 0 0 0 False 0 0 0 0 TN
chr20 34205619 34205960 1 1 0 0 False 1 1 0 0 TP
Expand Down Expand Up @@ -113,7 +113,7 @@ chr20 53913028 53913352 2 2 0 0 False 2 2 0 0 TP
chr20 54690771 54690873 2 2 0 0 False 2 2 0 0 TP
chr20 55532159 55533378 1 1 0 0 False 1 1 0 0 TP
chr20 55624482 55625807 6 6 6 0 True 11 11 0 0 TP
chr20 55627344 55628450 7 7 4 0 True 7 7 0 1 FP
chr20 55627344 55628450 7 7 4 0 True 8 8 0 0 TP
chr20 55943919 55945807 2 2 2 1 True 5 5 0 0 TP
chr20 56280422 56282114 4 4 5 1 True 10 10 0 0 TP
chr20 56284258 56284407 2 2 0 0 False 2 2 0 0 TP
Expand Down Expand Up @@ -172,7 +172,7 @@ chr20 62875172 62875556 2 2 3 0 True 3 3 0 0 TP
chr20 62975788 62976224 1 1 0 0 False 1 1 0 0 TP
chr20 62986310 62986805 2 2 0 0 False 2 2 0 0 TP
chr20 63027997 63028166 2 2 1 0 True 4 4 0 0 TP
chr20 63028876 63029402 2 2 0 1 True 1 1 0 1 FP
chr20 63028876 63029402 2 2 0 1 True 2 2 0 0 TP
chr20 63049033 63049412 3 3 1 0 True 2 2 0 0 TP
chr20 63068409 63068799 2 2 0 0 False 2 2 0 0 TP
chr20 63103249 63103492 1 1 0 0 False 1 1 0 0 TP
Expand Down Expand Up @@ -219,8 +219,8 @@ chr20 64090704 64091389 0 0 0 2 False 0 0 0 2 FP
chr20 64096658 64097164 0 0 0 2 False 0 0 0 2 FP
chr20 64125109 64127974 3 3 3 0 True 12 12 0 0 TP
chr20 64131804 64133955 5 5 8 1 True 24 24 0 0 TP
chr20 64134883 64136386 3 3 1 0 True 4 4 1 0 FN
chr20 64134883 64136386 3 3 1 0 True 4 4 0 0 TP
chr20 64157894 64158976 2 2 0 0 False 2 2 0 0 TP
chr20 64173409 64176529 4 4 7 3 True 18 18 0 0 TP
chr20 64173409 64176529 4 4 7 3 True 17 17 0 0 TP
chr20 64201854 64202098 3 3 0 0 False 3 3 0 0 TP
chr20 64233048 64233545 2 2 0 0 False 2 2 0 0 TP
18 changes: 9 additions & 9 deletions repo_utils/answer_key/refine/refine_output_one/refine.variant_summary.json
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@@ -1,11 +1,11 @@
{
"TP-base": 591,
"TP-comp": 591,
"FP": 18,
"FN": 3,
"precision": 0.9704433497536946,
"recall": 0.9949494949494949,
"f1": 0.9825436408977556,
"base cnt": 594,
"comp cnt": 609
"TP-base": 593,
"TP-comp": 593,
"FP": 15,
"FN": 2,
"precision": 0.975328947368421,
"recall": 0.9966386554621849,
"f1": 0.9858686616791356,
"base cnt": 595,
"comp cnt": 608
}
16 changes: 8 additions & 8 deletions repo_utils/answer_key/refine/refine_output_three/log.txt
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@@ -1,6 +1,6 @@
2023-11-01 14:06:18,612 [INFO] Truvari v4.1.1.dev0+a08d9a7.uc
2023-11-01 14:06:18,613 [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_three
2023-11-01 14:06:18,614 [INFO] Params:
2023-12-19 15:34:12,422 [INFO] Truvari v4.2.0rc1
2023-12-19 15:34:12,423 [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_three
2023-12-19 15:34:12,425 [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",
Expand Down Expand Up @@ -28,10 +28,10 @@
"check_monref": true,
"check_multi": true
}
2023-11-01 14:06:18,683 [INFO] Including 225 bed regions
2023-11-01 14:06:20,271 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855})
2023-11-01 14:06:20,272 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451})
2023-11-01 14:06:20,478 [INFO] Stats: {
2023-12-19 15:34:12,508 [INFO] Including 225 bed regions
2023-12-19 15:34:14,248 [INFO] Zipped 7158 variants Counter({'comp': 5303, 'base': 1855})
2023-12-19 15:34:14,250 [INFO] 212 chunks of 7158 variants Counter({'__filtered': 6120, 'base': 587, 'comp': 451})
2023-12-19 15:34:14,462 [INFO] Stats: {
"TP-base": 387,
"TP-comp": 387,
"FP": 64,
Expand Down Expand Up @@ -83,4 +83,4 @@
}
}
}
2023-11-01 14:06:20,479 [INFO] Finished bench
2023-12-19 15:34:14,463 [INFO] Finished bench
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2 changes: 1 addition & 1 deletion repo_utils/answer_key/refine/refine_output_three/phab_bench/params.json
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@@ -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/ce30u761.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single", "check_monref": true, "check_multi": true}
{"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/fqzb0b6u.bed", "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.7, "minhaplen": 50, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "syndip", "cSample": "p:HG002", "dup_to_ins": false, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": "a", "pick": "single", "check_monref": true, "check_multi": true}
22 changes: 11 additions & 11 deletions repo_utils/answer_key/refine/refine_output_three/phab_bench/summary.json
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Expand Up @@ -29,21 +29,21 @@
},
"weighted": {
"sequence": {
"TP": 120.4527998296544,
"FP": 9.857900094240904,
"FN": 17.068500188179314,
"precision": 0.9243508008168312,
"recall": 0.8758846797843979,
"f1": 0.8994653354032435,
"TP": 121.03439995925874,
"FP": 9.64990008994937,
"FN": 16.475100067444146,
"precision": 0.9261586886388359,
"recall": 0.8801893682673207,
"f1": 0.9025890973244014,
"total": 139
},
"size": {
"TP": 117.62869990803301,
"TP": 117.65679998137057,
"FP": 11.260100107640028,
"FN": 19.847500076517463,
"precision": 0.9126370940976192,
"recall": 0.8556295556703785,
"f1": 0.8832143855831983,
"FN": 19.819400003179908,
"precision": 0.9126561366285918,
"recall": 0.855833955219833,
"f1": 0.8833321880249987,
"total": 139
}
}
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30 changes: 16 additions & 14 deletions repo_utils/answer_key/refine/refine_output_three/refine.log.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
2023-11-01 14:06:22,093 [INFO] Truvari v4.1.1.dev0+a08d9a7.uc
2023-11-01 14:06:22,094 [INFO] Command /data/truvari/__main__.py refine --recount -U -r test_results/refine_output_three/candidate.refine.bed -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_three
2023-11-01 14:06:22,095 [INFO] Params:
2023-12-19 15:34:16,211 [INFO] Truvari v4.2.0rc1
2023-12-19 15:34:16,213 [INFO] Command /data/truvari/__main__.py refine --recount -U -r test_results/refine_output_three/candidate.refine.bed -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_three
2023-12-19 15:34:16,214 [INFO] Params:
{
"benchdir": "test_results/refine_output_three",
"reference": "repo_utils/test_files/refine_data/chr20.fa.gz",
Expand All @@ -13,14 +13,16 @@
"mafft_params": "--auto --thread 1",
"debug": false
}
2023-11-01 14:06:22,096 [INFO] Setting up regions
2023-11-01 14:06:22,144 [INFO] 92 --regions reduced to 92 after intersecting with 225 from --includebed
2023-11-01 14:06:22,523 [INFO] 41 regions to be refined
2023-11-01 14:06:22,532 [INFO] Preparing regions
2023-11-01 14:06:22,537 [INFO] Extracting haplotypes
2023-11-01 14:06:23,106 [INFO] Harmonizing variants
2023-11-01 14:06:24,655 [INFO] Running bench
2023-11-01 14:06:24,706 [INFO] Including 41 bed regions
2023-11-01 14:06:25,093 [INFO] Zipped 2844 variants Counter({'base': 1422, 'comp': 1422})
2023-11-01 14:06:25,094 [INFO] 35 chunks of 2844 variants Counter({'__filtered': 2595, 'base': 136, 'comp': 113})
2023-11-01 14:06:26,429 [INFO] Finished refine
2023-12-19 15:34:16,216 [INFO] Setting up regions
2023-12-19 15:34:16,264 [INFO] 92 --regions reduced to 92 after intersecting with 225 from --includebed
2023-12-19 15:34:16,681 [INFO] 41 regions to be refined
2023-12-19 15:34:16,691 [INFO] Preparing regions
2023-12-19 15:34:16,696 [INFO] Extracting haplotypes
2023-12-19 15:34:17,133 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
2023-12-19 15:34:17,155 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:883: CoverageWarning:No data was collected. (no-data-collected)
2023-12-19 15:34:17,169 [INFO] Harmonizing variants
2023-12-19 15:34:18,825 [INFO] Running bench
2023-12-19 15:34:18,872 [INFO] Including 41 bed regions
2023-12-19 15:34:19,325 [INFO] Zipped 2824 variants Counter({'base': 1412, 'comp': 1412})
2023-12-19 15:34:19,327 [INFO] 35 chunks of 2824 variants Counter({'__filtered': 2573, 'base': 136, 'comp': 115})
2023-12-19 15:34:20,774 [INFO] Finished refine
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