functest correction

ACEnglish · Jan 30, 2025 · 7dd8400 · 7dd8400
1 parent f019389
commit 7dd8400
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Showing 6 changed files with 17 additions and 10 deletions.
diff --git a/repo_utils/answer_key/bench/bench_unroll/log.txt b/repo_utils/answer_key/bench/bench_unroll/log.txt
@@ -1,6 +1,6 @@
-2025-01-06 03:04:00,136 [INFO] Truvari v5.0.0
-2025-01-06 03:04:00,137 [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/
-2025-01-06 03:04:00,138 [INFO] Params:
+2025-01-30 23:04:30,949 [INFO] Truvari v5.0.1.dev0+664fd5b
+2025-01-30 23:04:30,950 [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/
+2025-01-30 23:04:30,951 [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",
@@ -22,16 +22,23 @@
     "bnddist": 100,
     "sizemin": 50,
     "sizefilt": 30,
-    "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 03:04:00,182 [INFO] Zipped 71 variants Counter({'base': 43, 'comp': 28})
-2025-01-06 03:04:00,182 [INFO] 45 chunks of 71 variants Counter({'base': 43, 'comp': 28})
-2025-01-06 03:04:00,226 [INFO] Stats: {
+2025-01-30 23:04:31,028 [INFO] Zipped 71 variants Counter({'base': 43, 'comp': 28})
+2025-01-30 23:04:31,029 [INFO] 45 chunks of 71 variants Counter({'base': 43, 'comp': 28})
+2025-01-30 23:04:31,098 [INFO] Stats: {
     "TP-base": 18,
     "TP-comp": 18,
     "FP": 1,
@@ -58,4 +65,4 @@
         }
     }
 }
-2025-01-06 03:04:00,227 [INFO] Finished bench
+2025-01-30 23:04:31,099 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench_unroll/params.json b/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/", "includebed": null, "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": "NA12878", "cSample": "NULL", "dup_to_ins": false, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
+{"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, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "NA12878", "cSample": "NULL", "dup_to_ins": false, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "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}
diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_unroll/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_unroll/tp-comp.vcf.gz.tbi
Original file line number	Diff line number	Diff line change
		@@ -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/", "includebed": null, "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": "NA12878", "cSample": "NULL", "dup_to_ins": false, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
		{"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, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "NA12878", "cSample": "NULL", "dup_to_ins": false, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "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}