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refine progress
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@ACEnglish
ACEnglish committed Feb 2, 2025
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Showing 27 changed files with 341 additions and 423 deletions.
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27 changes: 17 additions & 10 deletions repo_utils/answer_key/refine/refine_output_one/log.txt
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2025-01-06 03:04:53,537 [INFO] Truvari v5.0.0
2025-01-06 03:04:53,537 [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
2025-01-06 03:04:53,538 [INFO] Params:
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:
{
"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 All @@ -22,17 +22,24 @@
"bnddist": 100,
"sizemin": 5,
"sizefilt": 5,
"sizemax": 50000,
"sizemax": -1,
"passonly": false,
"no_ref": false,
"pick": "single",
"ignore_monref": true,
"check_multi": true,
"check_monref": true,
"check_multi": true
"no_single_bnd": true,
"write_resolved": false,
"decompose": true,
"short_circuit": false,
"skip_gt": false,
"max_resolve": 25000
}
2025-01-06 03:04:53,572 [INFO] Including 225 bed regions
2025-01-06 03:04:55,638 [INFO] Zipped 7157 variants Counter({'comp': 5302, 'base': 1855})
2025-01-06 03:04:55,638 [INFO] 211 chunks of 7157 variants Counter({'__filtered': 6137, 'base': 569, 'comp': 451})
2025-01-06 03:04:55,718 [INFO] Stats: {
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: {
"TP-base": 387,
"TP-comp": 387,
"FP": 64,
Expand Down Expand Up @@ -64,4 +71,4 @@
}
}
}
2025-01-06 03:04:55,718 [INFO] Finished bench
2025-02-02 06:13:49,324 [INFO] Finished bench
2 changes: 1 addition & 1 deletion repo_utils/answer_key/refine/refine_output_one/params.json
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{"base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", "output": "test_results/refine_output_one", "includebed": "/data/repo_utils/test_files/refine_data/h1_hc_tr_hg002.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": "HG002", "dup_to_ins": false, "bnddist": 100, "sizemin": 5, "sizefilt": 5, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
{"base": "/data/repo_utils/test_files/refine_data/hg002_base.vcf.gz", "comp": "/data/repo_utils/test_files/refine_data/hg002_comp.vcf.gz", "output": "test_results/refine_output_one", "includebed": "/data/repo_utils/test_files/refine_data/h1_hc_tr_hg002.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": "HG002", "dup_to_ins": false, "bnddist": 100, "sizemin": 5, "sizefilt": 5, "sizemax": -1, "passonly": false, "no_ref": false, "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": true, "short_circuit": false, "skip_gt": false, "max_resolve": 25000}
2 changes: 1 addition & 1 deletion repo_utils/answer_key/refine/refine_output_one/phab_bench/candidate.refine.bed
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chr20 5040466 5040487
chr20 5041931 5042443
chr20 16257844 16259215
chr20 16257844 16259455
chr20 32723034 32723055
chr20 51953809 51953830
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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/in6rjnqm.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": 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/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}
24 changes: 12 additions & 12 deletions repo_utils/answer_key/refine/refine_output_one/phab_bench/summary.json
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{
"TP-base": 359,
"TP-comp": 359,
"FP": 4,
"TP-base": 361,
"TP-comp": 361,
"FP": 5,
"FN": 2,
"precision": 0.9889807162534435,
"recall": 0.9944598337950139,
"f1": 0.9917127071823205,
"base cnt": 361,
"comp cnt": 363,
"TP-comp_TP-gt": 359,
"precision": 0.9863387978142076,
"recall": 0.9944903581267218,
"f1": 0.9903978052126201,
"base cnt": 363,
"comp cnt": 366,
"TP-comp_TP-gt": 361,
"TP-comp_FP-gt": 0,
"TP-base_TP-gt": 359,
"TP-base_TP-gt": 361,
"TP-base_FP-gt": 0,
"gt_concordance": 1.0,
"gt_matrix": {
"(0, 1)": {
"(1, 0)": 135
"(1, 0)": 136
},
"(1, 0)": {
"(0, 1)": 177
"(0, 1)": 178
},
"(1, 1)": {
"(1, 1)": 47
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47 changes: 26 additions & 21 deletions repo_utils/answer_key/refine/refine_output_one/refine.log.txt
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2025-01-06 03:04:56,953 [INFO] Truvari v5.0.0
2025-01-06 03:04:56,953 [INFO] Command /data/truvari/__main__.py refine -u -f repo_utils/test_files/refine_data/chr20.fa.gz test_results/refine_output_one
2025-01-06 03:04:56,954 [INFO] Params:
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:
{
"benchdir": "test_results/refine_output_one",
"reference": "repo_utils/test_files/refine_data/chr20.fa.gz",
"regions": null,
"align": "mafft",
"use_original_vcfs": true,
"use_region_coords": false,
"recount": false,
"write_phab": true,
"threads": 4,
"align": "mafft",
"buffer": 100,
"reference": "repo_utils/test_files/refine_data/chr20.fa.gz",
"regions": null,
"coords": "O",
"subset": false,
"mafft_params": "--auto --thread 1",
"debug": false
}
2025-01-06 03:04:56,954 [INFO] Setting up regions
2025-01-06 03:04:56,964 [INFO] Evaluating 225 regions
2025-01-06 03:04:57,464 [INFO] 75 regions to be refined
2025-01-06 03:04:57,473 [INFO] Preparing regions
2025-01-06 03:04:57,480 [INFO] Extracting haplotypes
2025-01-06 03:04:57,954 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:888: CoverageWarning:No data was collected. (no-data-collected)
2025-01-06 03:04:57,956 [WARNING] /usr/local/lib/python3.10/dist-packages/coverage/control.py:888: CoverageWarning:No data was collected. (no-data-collected)
2025-01-06 03:04:57,966 [INFO] Harmonizing variants
2025-01-06 03:04:59,358 [INFO] Running bench
2025-01-06 03:04:59,376 [INFO] Including 75 bed regions
2025-01-06 03:05:00,104 [INFO] Zipped 3930 variants Counter({'base': 1965, 'comp': 1965})
2025-01-06 03:05:00,104 [INFO] 76 chunks of 3930 variants Counter({'__filtered': 3206, 'comp': 363, 'base': 361})
2025-01-06 03:05:00,365 [INFO] Finished refine
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
16 changes: 8 additions & 8 deletions repo_utils/answer_key/refine/refine_output_one/refine.region_summary.json
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{
"TP": 199,
"TN": 14,
"FP": 10,
"TN": 13,
"FP": 11,
"FN": 2,
"base P": 202,
"base N": 23,
"base N": 22,
"comp P": 210,
"comp N": 15,
"comp N": 14,
"PPV": 0.9476190476190476,
"TPR": 0.9851485148514851,
"TNR": 0.6086956521739131,
"NPV": 0.9333333333333333,
"ACC": 0.9466666666666667,
"BA": 0.7969220835126991,
"TNR": 0.5909090909090909,
"NPV": 0.9285714285714286,
"ACC": 0.9464285714285714,
"BA": 0.788028802880288,
"F1": 0.9660194174757282,
"UND": 0
}
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