From 3150ee654ab69f9ca3e5942db6e26edb4eb4cc10 Mon Sep 17 00:00:00 2001 From: Adam English Date: Thu, 1 Aug 2024 19:49:31 -0400 Subject: [PATCH] correctly filtering star alleles --- .../bench_starallele/candidate.refine.bed | 1 + .../bench/bench_starallele/fn.vcf.gz | Bin 0 -> 2192 bytes .../bench/bench_starallele/fn.vcf.gz.tbi | Bin 0 -> 128 bytes .../bench/bench_starallele/fp.vcf.gz | Bin 0 -> 1814 bytes .../bench/bench_starallele/fp.vcf.gz.tbi | Bin 0 -> 129 bytes .../answer_key/bench/bench_starallele/log.txt | 50 ++++++++++++++++++ .../bench/bench_starallele/params.json | 1 + .../bench/bench_starallele/summary.json | 17 ++++++ .../bench/bench_starallele/tp-base.vcf.gz | Bin 0 -> 1608 bytes .../bench/bench_starallele/tp-base.vcf.gz.tbi | Bin 0 -> 72 bytes .../bench/bench_starallele/tp-comp.vcf.gz | Bin 0 -> 1606 bytes .../bench/bench_starallele/tp-comp.vcf.gz.tbi | Bin 0 -> 72 bytes repo_utils/sub_tests/bench.sh | 7 +++ .../test_files/variants/star.base.vcf.gz | Bin 0 -> 1812 bytes .../test_files/variants/star.base.vcf.gz.tbi | Bin 0 -> 129 bytes .../test_files/variants/star.comp.vcf.gz | Bin 0 -> 1543 bytes .../test_files/variants/star.comp.vcf.gz.tbi | Bin 0 -> 128 bytes truvari/matching.py | 2 +- 18 files changed, 77 insertions(+), 1 deletion(-) create mode 100644 repo_utils/answer_key/bench/bench_starallele/candidate.refine.bed create mode 100644 repo_utils/answer_key/bench/bench_starallele/fn.vcf.gz create mode 100644 repo_utils/answer_key/bench/bench_starallele/fn.vcf.gz.tbi create mode 100644 repo_utils/answer_key/bench/bench_starallele/fp.vcf.gz create mode 100644 repo_utils/answer_key/bench/bench_starallele/fp.vcf.gz.tbi create mode 100644 repo_utils/answer_key/bench/bench_starallele/log.txt create mode 100644 repo_utils/answer_key/bench/bench_starallele/params.json create mode 100644 repo_utils/answer_key/bench/bench_starallele/summary.json create mode 100644 repo_utils/answer_key/bench/bench_starallele/tp-base.vcf.gz create mode 100644 repo_utils/answer_key/bench/bench_starallele/tp-base.vcf.gz.tbi create mode 100644 repo_utils/answer_key/bench/bench_starallele/tp-comp.vcf.gz create mode 100644 repo_utils/answer_key/bench/bench_starallele/tp-comp.vcf.gz.tbi create mode 100644 repo_utils/test_files/variants/star.base.vcf.gz create mode 100644 repo_utils/test_files/variants/star.base.vcf.gz.tbi create mode 100644 repo_utils/test_files/variants/star.comp.vcf.gz create mode 100644 repo_utils/test_files/variants/star.comp.vcf.gz.tbi diff --git a/repo_utils/answer_key/bench/bench_starallele/candidate.refine.bed b/repo_utils/answer_key/bench/bench_starallele/candidate.refine.bed new file mode 100644 index 00000000..015059aa --- /dev/null +++ b/repo_utils/answer_key/bench/bench_starallele/candidate.refine.bed @@ -0,0 +1 @@ +chr1 6004926 6005445 \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench_starallele/fn.vcf.gz b/repo_utils/answer_key/bench/bench_starallele/fn.vcf.gz new file mode 100644 index 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19:48:18,700 [INFO] Params: +{ + "base": "/Users/english/code/truvari/repo_utils/test_files/variants/star.base.vcf.gz", + "comp": "/Users/english/code/truvari/repo_utils/test_files/variants/star.comp.vcf.gz", + "output": "test_results/bench_starallele/", + "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": "HG002", + "cSample": "HG002", + "dup_to_ins": false, + "sizemin": 0, + "sizefilt": 0, + "sizemax": 50000, + "passonly": false, + "no_ref": false, + "pick": "single", + "check_monref": true, + "check_multi": true +} +2024-08-01 19:48:18,705 [INFO] Zipped 7 variants Counter({'base': 6, 'comp': 1}) +2024-08-01 19:48:18,705 [INFO] 1 chunks of 7 variants Counter({'base': 5, '__filtered': 1, 'comp': 1}) +2024-08-01 19:48:18,721 [INFO] Stats: { + "TP-base": 0, + "TP-comp": 0, + "FP": 1, + "FN": 5, + "precision": 0.0, + "recall": 0.0, + "f1": null, + "base cnt": 5, + "comp cnt": 1, + "TP-comp_TP-gt": 0, + "TP-comp_FP-gt": 0, + "TP-base_TP-gt": 0, + "TP-base_FP-gt": 0, + "gt_concordance": 0, + "gt_matrix": {} +} +2024-08-01 19:48:18,721 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench_starallele/params.json b/repo_utils/answer_key/bench/bench_starallele/params.json new file mode 100644 index 00000000..5b9a1694 --- /dev/null +++ b/repo_utils/answer_key/bench/bench_starallele/params.json @@ -0,0 +1 @@ +{"base": "/Users/english/code/truvari/repo_utils/test_files/variants/star.base.vcf.gz", "comp": "/Users/english/code/truvari/repo_utils/test_files/variants/star.comp.vcf.gz", "output": "test_results/bench_starallele/", "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": "HG002", "cSample": "HG002", "dup_to_ins": false, "sizemin": 0, 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