decomp prototype finished

looks like it works
ACEnglish · Jan 9, 2025 · 3da688f · 3da688f
1 parent c1311f7
commit 3da688f
Show file tree

Hide file tree

Showing 29 changed files with 20,777 additions and 1,135 deletions.
diff --git a/repo_utils/answer_key/bench/bench_bnd/candidate.refine.bed b/repo_utils/answer_key/bench/bench_bnd/candidate.refine.bed
@@ -1,24 +1,37 @@
 chr1	181135	181156
 chr1	6005049	6006670
+chr1	122627325	122627346
 chr1	224013761	224013782
 chr10	1238267	1238288
 chr10	39478703	39478724
+chr10	67470500	67470521
+chr10	68211488	68211509
 chr10	132505641	132506422
 chr11	964817	964838
+chr11	33648565	33648586
 chr11	44662925	44662946
 chr11	48880455	48880476
 chr11	48888289	48888310
-chr11	68232223	68232244
+chr11	68232220	68233087
 chr11	80583401	80583422
-chr11	105902622	105902643
+chr11	105902622	105902647
+chr11	125661462	125661483
+chr11	135076371	135076392
 chr12	2572354	2572375
 chr12	10428997	10444441
+chr12	24759747	24759768
 chr12	26566549	26566649
-chr12	106703356	106718437
+chr12	26706109	26706130
+chr12	106703356	106718439
 chr12	132242311	132242332
 chr13	56380894	56381040
 chr13	114073358	114074122
 chr14	102919538	102919632
+chr15	31496974	31496995
+chr15	31637303	31637324
+chr15	40450778	40450800
+chr15	44117194	44117215
+chr15	44248462	44248483
 chr15	74894096	74894117
 chr16	1025231	1025252
 chr16	49626994	49627100
@@ -27,38 +40,64 @@ chr17	31964205	32004138
 chr17	77850848	77850938
 chr17	83120464	83120485
 chr17	83127668	83127689
+chr18	28481412	28481433
+chr18	28482559	28482580
 chr18	70465189	70465210
 chr18	78390326	78390347
 chr19	395626	395835
 chr19	3477781	3477868
 chr19	29439299	29439424
 chr19	38981201	38983536
+chr19	53185919	53185940
 chr19	55068010	55068465
 chr2	9737589	9737610
+chr2	80358794	80358815
 chr2	138335007	138335083
 chr2	157917136	157917157
 chr2	238119351	238119427
+chr2	242182777	242182798
 chr20	16410045	16410066
+chr20	25499107	25499128
 chr20	38428231	38428252
+chr20	38430124	38430145
+chr20	62257534	62257555
+chr20	62378058	62378079
 chr20	62755268	62755289
 chr20	63443033	63443054
 chr22	31903282	31903303
 chr22	45328219	45328240
 chr22	47732364	47732476
 chr22	49494347	49494368
+chr3	11399	11532
 chr3	112164423	112164444
+chr3	138126516	138126537
 chr3	184714589	184714610
+chr3	192188379	192188404
 chr4	1429347	1434609
 chr4	8631479	8637158
+chr5	36023169	36023190
+chr5	39360014	39360035
 chr5	71009525	71015235
+chr5	172418408	172418429
+chr5	172626365	172626386
 chr5	176031036	176031057
+chr6	131707570	131707591
+chr6	157972782	157972814
+chr7	4824638	4824659
+chr7	7802502	7802523
 chr7	23502979	23503000
 chr7	68922678	68950323
 chr7	75988853	75988924
+chr7	144186929	144186950
 chr7	158151440	158151461
 chr8	48193098	48193205
 chr8	77023596	77040442
 chr8	143669349	143669370
 chr9	104414084	104414105
 chr9	136535716	136535737
-chrX	125901244	125901387
+chrX	90627638	90627659
+chrX	95207229	95207250
+chrX	95810791	95810812
+chrX	95812857	95812878
+chrX	125901244	125901387
+chrY	9591875	9591896
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
diff --git a/repo_utils/answer_key/bench/bench_bnd/log.txt b/repo_utils/answer_key/bench/bench_bnd/log.txt
diff --git a/repo_utils/answer_key/bench/bench_bnd/params.json b/repo_utils/answer_key/bench/bench_bnd/params.json
@@ -1 +1 @@
-{"base": "/data/repo_utils/test_files/variants/bnd.base.vcf.gz", "comp": "/data/repo_utils/test_files/variants/bnd.comp.vcf.gz", "output": "test_results/bench_bnd/", "includebed": null, "extend": 0, "debug": true, "reference": null, "refdist": 500, "pctseq": 0.0, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "HG008-T", "cSample": "HG008_T_hiphase.haplotagged", "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": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.base.vcf.gz", "comp": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.comp.vcf.gz", "output": "test_results/bench_bnd/", "includebed": null, "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.0, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "HG008-T", "cSample": "HG008_T_hiphase.haplotagged", "dup_to_ins": false, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": false, "short_circuit": false, "skip_gt": false}
diff --git a/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz.tbi
diff --git a/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz
diff --git a/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz.tbi
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"base": "/data/repo_utils/test_files/variants/bnd.base.vcf.gz", "comp": "/data/repo_utils/test_files/variants/bnd.comp.vcf.gz", "output": "test_results/bench_bnd/", "includebed": null, "extend": 0, "debug": true, "reference": null, "refdist": 500, "pctseq": 0.0, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "HG008-T", "cSample": "HG008_T_hiphase.haplotagged", "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": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.base.vcf.gz", "comp": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.comp.vcf.gz", "output": "test_results/bench_bnd/", "includebed": null, "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.0, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "HG008-T", "cSample": "HG008_T_hiphase.haplotagged", "dup_to_ins": false, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": false, "short_circuit": false, "skip_gt": false}