Sparse Annotations

Matching annotations (e.g. `PctSeqSimilarity`) with value of None are no longer written outputs.
ACEnglish · Jan 6, 2025 · 3e74d9f · 3e74d9f
1 parent 8f02ec9
commit 3e74d9f
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Showing 172 changed files with 2,889 additions and 1,923 deletions.
diff --git a/repo_utils/answer_key/bench/bench12/fn.vcf.gz b/repo_utils/answer_key/bench/bench12/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12/fp.vcf.gz b/repo_utils/answer_key/bench/bench12/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/fp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12/log.txt b/repo_utils/answer_key/bench/bench12/log.txt
@@ -1,6 +1,6 @@
-2024-11-14 05:19:41,035 [INFO] Truvari v5.0.0
-2024-11-14 05:19:41,036 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench12/
-2024-11-14 05:19:41,037 [INFO] Params:
+2025-01-06 03:03:52,435 [INFO] Truvari v5.0.0
+2025-01-06 03:03:52,435 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench12/
+2025-01-06 03:03:52,436 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz",
@@ -14,10 +14,12 @@
     "pctsize": 0.7,
     "pctovl": 0.0,
     "typeignore": false,
+    "no_roll": true,
     "chunksize": 1000,
     "bSample": "NA24385",
     "cSample": "NA12878",
     "dup_to_ins": true,
+    "bnddist": 100,
     "sizemin": 50,
     "sizefilt": 30,
     "sizemax": 50000,
@@ -27,9 +29,9 @@
     "check_monref": true,
     "check_multi": true
 }
-2024-11-14 05:19:41,255 [INFO] Zipped 3936 variants Counter({'base': 2153, 'comp': 1783})
-2024-11-14 05:19:41,256 [INFO] 12 chunks of 3936 variants Counter({'__filtered': 3904, 'base': 18, 'comp': 14})
-2024-11-14 05:19:41,298 [INFO] Stats: {
+2025-01-06 03:03:52,680 [INFO] Zipped 3936 variants Counter({'base': 2153, 'comp': 1783})
+2025-01-06 03:03:52,681 [INFO] 12 chunks of 3936 variants Counter({'__filtered': 3904, 'base': 18, 'comp': 14})
+2025-01-06 03:03:52,717 [INFO] Stats: {
     "TP-base": 8,
     "TP-comp": 8,
     "FP": 3,
@@ -60,4 +62,4 @@
         }
     }
 }
-2024-11-14 05:19:41,298 [INFO] Finished bench
+2025-01-06 03:03:52,718 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench12/params.json b/repo_utils/answer_key/bench/bench12/params.json
@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA24385", "cSample": "NA12878", "dup_to_ins": true, "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/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "NA24385", "cSample": "NA12878", "dup_to_ins": true, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
diff --git a/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12/tp-comp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz b/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/fp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/log.txt b/repo_utils/answer_key/bench/bench12_gtcomp/log.txt
@@ -1,6 +1,6 @@
-2024-11-14 05:19:49,314 [INFO] Truvari v5.0.0
-2024-11-14 05:19:49,315 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench12_gtcomp/ --pick ac
-2024-11-14 05:19:49,315 [INFO] Params:
+2025-01-06 03:04:01,383 [INFO] Truvari v5.0.0
+2025-01-06 03:04:01,383 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input2.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench12_gtcomp/ --pick ac
+2025-01-06 03:04:01,384 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz",
@@ -14,10 +14,12 @@
     "pctsize": 0.7,
     "pctovl": 0.0,
     "typeignore": false,
+    "no_roll": true,
     "chunksize": 1000,
     "bSample": "NA24385",
     "cSample": "NA12878",
     "dup_to_ins": true,
+    "bnddist": 100,
     "sizemin": 50,
     "sizefilt": 30,
     "sizemax": 50000,
@@ -27,9 +29,9 @@
     "check_monref": true,
     "check_multi": true
 }
-2024-11-14 05:19:49,531 [INFO] Zipped 3936 variants Counter({'base': 2153, 'comp': 1783})
-2024-11-14 05:19:49,532 [INFO] 12 chunks of 3936 variants Counter({'__filtered': 3904, 'base': 18, 'comp': 14})
-2024-11-14 05:19:49,574 [INFO] Stats: {
+2025-01-06 03:04:01,649 [INFO] Zipped 3936 variants Counter({'base': 2153, 'comp': 1783})
+2025-01-06 03:04:01,650 [INFO] 12 chunks of 3936 variants Counter({'__filtered': 3904, 'base': 18, 'comp': 14})
+2025-01-06 03:04:01,689 [INFO] Stats: {
     "TP-base": 9,
     "TP-comp": 8,
     "FP": 3,
@@ -60,4 +62,4 @@
         }
     }
 }
-2024-11-14 05:19:49,574 [INFO] Finished bench
+2025-01-06 03:04:01,690 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/params.json b/repo_utils/answer_key/bench/bench12_gtcomp/params.json
@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12_gtcomp/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA24385", "cSample": "NA12878", "dup_to_ins": true, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "ac", "check_monref": true, "check_multi": true}
+{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12_gtcomp/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "NA24385", "cSample": "NA12878", "dup_to_ins": true, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "ac", "check_monref": true, "check_multi": true}
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench12_gtcomp/tp-comp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13/fp.vcf.gz b/repo_utils/answer_key/bench/bench13/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/fp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13/log.txt b/repo_utils/answer_key/bench/bench13/log.txt
@@ -1,6 +1,6 @@
-2024-11-14 05:19:42,526 [INFO] Truvari v5.0.0
-2024-11-14 05:19:42,527 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13/
-2024-11-14 05:19:42,527 [INFO] Params:
+2025-01-06 03:03:53,974 [INFO] Truvari v5.0.0
+2025-01-06 03:03:53,975 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13/
+2025-01-06 03:03:53,975 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz",
@@ -14,10 +14,12 @@
     "pctsize": 0.7,
     "pctovl": 0.0,
     "typeignore": false,
+    "no_roll": true,
     "chunksize": 1000,
     "bSample": "NA24385",
     "cSample": "HG00733",
     "dup_to_ins": true,
+    "bnddist": 100,
     "sizemin": 50,
     "sizefilt": 30,
     "sizemax": 50000,
@@ -27,9 +29,9 @@
     "check_monref": true,
     "check_multi": true
 }
-2024-11-14 05:19:42,759 [INFO] Zipped 4218 variants Counter({'base': 2153, 'comp': 2065})
-2024-11-14 05:19:42,759 [INFO] 14 chunks of 4218 variants Counter({'__filtered': 4179, 'comp': 21, 'base': 18})
-2024-11-14 05:19:42,801 [INFO] Stats: {
+2025-01-06 03:03:54,559 [INFO] Zipped 4218 variants Counter({'base': 2153, 'comp': 2065})
+2025-01-06 03:03:54,560 [INFO] 14 chunks of 4218 variants Counter({'__filtered': 4179, 'comp': 21, 'base': 18})
+2025-01-06 03:03:54,606 [INFO] Stats: {
     "TP-base": 10,
     "TP-comp": 10,
     "FP": 7,
@@ -59,4 +61,4 @@
         }
     }
 }
-2024-11-14 05:19:42,802 [INFO] Finished bench
+2025-01-06 03:03:54,607 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench13/params.json b/repo_utils/answer_key/bench/bench13/params.json
@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench13/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA24385", "cSample": "HG00733", "dup_to_ins": true, "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/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench13/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "NA24385", "cSample": "HG00733", "dup_to_ins": true, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
diff --git a/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13/tp-comp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_extend/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_extend/fp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_extend/log.txt b/repo_utils/answer_key/bench/bench13_extend/log.txt
@@ -1,6 +1,6 @@
-2024-11-14 05:19:46,721 [INFO] Truvari v5.0.0
-2024-11-14 05:19:46,722 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13_extend/ --includebed repo_utils/test_files/beds/include.bed --extend 500
-2024-11-14 05:19:46,722 [INFO] Params:
+2025-01-06 03:03:58,792 [INFO] Truvari v5.0.0
+2025-01-06 03:03:58,793 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13_extend/ --includebed repo_utils/test_files/beds/include.bed --extend 500
+2025-01-06 03:03:58,794 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz",
@@ -14,10 +14,12 @@
     "pctsize": 0.7,
     "pctovl": 0.0,
     "typeignore": false,
+    "no_roll": true,
     "chunksize": 1000,
     "bSample": "NA24385",
     "cSample": "HG00733",
     "dup_to_ins": true,
+    "bnddist": 100,
     "sizemin": 50,
     "sizefilt": 30,
     "sizemax": 50000,
@@ -27,13 +29,13 @@
     "check_monref": true,
     "check_multi": true
 }
-2024-11-14 05:19:46,736 [INFO] Including 11 bed regions
-2024-11-14 05:19:46,737 [INFO] Found 1 chromosomes with overlapping regions
-2024-11-14 05:19:46,738 [INFO] Extending the regions by 500 bases
-2024-11-14 05:19:46,739 [INFO] Found 1 chromosomes with overlapping regions
-2024-11-14 05:19:46,851 [INFO] Zipped 2052 variants Counter({'base': 1132, 'comp': 920})
-2024-11-14 05:19:46,852 [INFO] 10 chunks of 2052 variants Counter({'__filtered': 2025, 'comp': 15, 'base': 12})
-2024-11-14 05:19:46,896 [INFO] Stats: {
+2025-01-06 03:03:58,809 [INFO] Including 11 bed regions
+2025-01-06 03:03:58,810 [INFO] Found 1 chromosomes with overlapping regions
+2025-01-06 03:03:58,810 [INFO] Extending the regions by 500 bases
+2025-01-06 03:03:58,812 [INFO] Found 1 chromosomes with overlapping regions
+2025-01-06 03:03:58,942 [INFO] Zipped 2052 variants Counter({'base': 1132, 'comp': 920})
+2025-01-06 03:03:58,942 [INFO] 10 chunks of 2052 variants Counter({'__filtered': 2025, 'comp': 15, 'base': 12})
+2025-01-06 03:03:58,979 [INFO] Stats: {
     "TP-base": 6,
     "TP-comp": 6,
     "FP": 4,
@@ -62,4 +64,4 @@
         }
     }
 }
-2024-11-14 05:19:46,897 [INFO] Finished bench
+2025-01-06 03:03:58,979 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench13_extend/params.json b/repo_utils/answer_key/bench/bench13_extend/params.json
@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench13_extend/", "includebed": "/data/repo_utils/test_files/beds/include.bed", "extend": 500, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA24385", "cSample": "HG00733", "dup_to_ins": true, "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/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench13_extend/", "includebed": "/data/repo_utils/test_files/beds/include.bed", "extend": 500, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "NA24385", "cSample": "HG00733", "dup_to_ins": true, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
diff --git a/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_extend/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_extend/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_extend/tp-comp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz b/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_includebed/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_includebed/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_includebed/fp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_includebed/log.txt b/repo_utils/answer_key/bench/bench13_includebed/log.txt
@@ -1,6 +1,6 @@
-2024-11-14 05:19:45,386 [INFO] Truvari v5.0.0
-2024-11-14 05:19:45,387 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13_includebed/ --includebed repo_utils/test_files/beds/include.bed
-2024-11-14 05:19:45,388 [INFO] Params:
+2025-01-06 03:03:57,421 [INFO] Truvari v5.0.0
+2025-01-06 03:03:57,421 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input1.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench13_includebed/ --includebed repo_utils/test_files/beds/include.bed
+2025-01-06 03:03:57,422 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input1.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz",
@@ -14,10 +14,12 @@
     "pctsize": 0.7,
     "pctovl": 0.0,
     "typeignore": false,
+    "no_roll": true,
     "chunksize": 1000,
     "bSample": "NA24385",
     "cSample": "HG00733",
     "dup_to_ins": true,
+    "bnddist": 100,
     "sizemin": 50,
     "sizefilt": 30,
     "sizemax": 50000,
@@ -27,11 +29,11 @@
     "check_monref": true,
     "check_multi": true
 }
-2024-11-14 05:19:45,402 [INFO] Including 11 bed regions
-2024-11-14 05:19:45,403 [INFO] Found 1 chromosomes with overlapping regions
-2024-11-14 05:19:45,507 [INFO] Zipped 2032 variants Counter({'base': 1132, 'comp': 900})
-2024-11-14 05:19:45,508 [INFO] 9 chunks of 2032 variants Counter({'__filtered': 2009, 'base': 12, 'comp': 11})
-2024-11-14 05:19:45,551 [INFO] Stats: {
+2025-01-06 03:03:57,439 [INFO] Including 11 bed regions
+2025-01-06 03:03:57,440 [INFO] Found 1 chromosomes with overlapping regions
+2025-01-06 03:03:57,568 [INFO] Zipped 2032 variants Counter({'base': 1132, 'comp': 900})
+2025-01-06 03:03:57,568 [INFO] 9 chunks of 2032 variants Counter({'__filtered': 2009, 'base': 12, 'comp': 11})
+2025-01-06 03:03:57,606 [INFO] Stats: {
     "TP-base": 5,
     "TP-comp": 5,
     "FP": 4,
@@ -57,4 +59,4 @@
         }
     }
 }
-2024-11-14 05:19:45,552 [INFO] Finished bench
+2025-01-06 03:03:57,607 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench13_includebed/params.json b/repo_utils/answer_key/bench/bench13_includebed/params.json
@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench13_includebed/", "includebed": "/data/repo_utils/test_files/beds/include.bed", "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA24385", "cSample": "HG00733", "dup_to_ins": true, "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/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench13_includebed/", "includebed": "/data/repo_utils/test_files/beds/include.bed", "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "NA24385", "cSample": "HG00733", "dup_to_ins": true, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}
diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_includebed/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench13_includebed/tp-comp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench23/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench23/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench23/fp.vcf.gz b/repo_utils/answer_key/bench/bench23/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench23/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench23/fp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench23/log.txt b/repo_utils/answer_key/bench/bench23/log.txt
@@ -1,6 +1,6 @@
-2024-11-14 05:19:43,968 [INFO] Truvari v5.0.0
-2024-11-14 05:19:43,968 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input2.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench23/ --pick multi
-2024-11-14 05:19:43,969 [INFO] Params:
+2025-01-06 03:03:55,867 [INFO] Truvari v5.0.0
+2025-01-06 03:03:55,868 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/input2.vcf.gz -c repo_utils/test_files/variants/input3.vcf.gz -f repo_utils/test_files/references/reference.fa --dup-to-ins -o test_results/bench23/ --pick multi
+2025-01-06 03:03:55,868 [INFO] Params:
 {
     "base": "/data/repo_utils/test_files/variants/input2.vcf.gz",
     "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz",
@@ -14,10 +14,12 @@
     "pctsize": 0.7,
     "pctovl": 0.0,
     "typeignore": false,
+    "no_roll": true,
     "chunksize": 1000,
     "bSample": "NA12878",
     "cSample": "HG00733",
     "dup_to_ins": true,
+    "bnddist": 100,
     "sizemin": 50,
     "sizefilt": 30,
     "sizemax": 50000,
@@ -27,9 +29,9 @@
     "check_monref": true,
     "check_multi": true
 }
-2024-11-14 05:19:44,175 [INFO] Zipped 3848 variants Counter({'comp': 2065, 'base': 1783})
-2024-11-14 05:19:44,175 [INFO] 14 chunks of 3848 variants Counter({'__filtered': 3816, 'comp': 21, 'base': 11})
-2024-11-14 05:19:44,219 [INFO] Stats: {
+2025-01-06 03:03:56,138 [INFO] Zipped 3848 variants Counter({'comp': 2065, 'base': 1783})
+2025-01-06 03:03:56,139 [INFO] 14 chunks of 3848 variants Counter({'__filtered': 3816, 'comp': 21, 'base': 11})
+2025-01-06 03:03:56,175 [INFO] Stats: {
     "TP-base": 7,
     "TP-comp": 8,
     "FP": 9,
@@ -55,4 +57,4 @@
         }
     }
 }
-2024-11-14 05:19:44,219 [INFO] Finished bench
+2025-01-06 03:03:56,175 [INFO] Finished bench
diff --git a/repo_utils/answer_key/bench/bench23/params.json b/repo_utils/answer_key/bench/bench23/params.json
@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/input2.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench23/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA12878", "cSample": "HG00733", "dup_to_ins": true, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "multi", "check_monref": true, "check_multi": true}
+{"base": "/data/repo_utils/test_files/variants/input2.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input3.vcf.gz", "output": "test_results/bench23/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "NA12878", "cSample": "HG00733", "dup_to_ins": true, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "multi", "check_monref": true, "check_multi": true}
diff --git a/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench23/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench23/tp-comp.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz b/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz b/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz.tbi
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"base": "/data/repo_utils/test_files/variants/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "chunksize": 1000, "bSample": "NA24385", "cSample": "NA12878", "dup_to_ins": true, "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/input1.vcf.gz", "comp": "/data/repo_utils/test_files/variants/input2.vcf.gz", "output": "test_results/bench12/", "includebed": null, "extend": 0, "debug": false, "reference": "/data/repo_utils/test_files/references/reference.fa", "refdist": 500, "pctseq": 0.7, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "NA24385", "cSample": "NA12878", "dup_to_ins": true, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true}