fix decomp BND

repo_utils/answer_key/bench/bench_bnd/candidate.refine.bed

@@ -37,6 +37,7 @@ chr16	1025231	1025252
 chr16	49626994	49627100
 chr16	89536459	89536480
 chr17	31964205	32004138
+chr17	32670386	32670407
 chr17	77850848	77850938
 chr17	83120464	83120485
 chr17	83127668	83127689
@@ -46,12 +47,14 @@ chr18	70465189	70465210
 chr18	78390326	78390347
 chr19	395626	395835
 chr19	3477781	3477868
+chr19	11196125	11218966
 chr19	29439299	29439424
-chr19	38981201	38983536
+chr19	44991097	44991118
 chr19	53185919	53185940
 chr19	55068010	55068465
 chr2	9737589	9737610
 chr2	80358794	80358815
+chr2	80401493	80401514
 chr2	138335007	138335083
 chr2	157917136	157917157
 chr2	238119351	238119427
@@ -86,7 +89,7 @@ chr6	157972782	157972814
 chr7	4824638	4824659
 chr7	7802502	7802523
 chr7	23502979	23503000
-chr7	68922678	68950323
+chr7	68922678	68922699
 chr7	75988853	75988924
 chr7	144186929	144186950
 chr7	158151440	158151461

repo_utils/answer_key/bench/bench_bnd/log.txt

@@ -1,6 +1,6 @@
-2025-01-08 19:03:15,280 [INFO] Truvari v5.0.0
-2025-01-08 19:03:15,280 [INFO] Command /Users/english/code/truvari/truvari/__main__.py bench -b repo_utils/test_files/variants/bnd.base.vcf.gz -c repo_utils/test_files/variants/bnd.comp.vcf.gz -p 0 -o test_results/bench_bnd/ --no-decompose
-2025-01-08 19:03:15,280 [INFO] Params:
+2025-01-08 20:16:32,128 [INFO] Truvari v5.0.0
+2025-01-08 20:16:32,129 [INFO] Command /Users/english/code/truvari/truvari/__main__.py bench -b repo_utils/test_files/variants/bnd.base.vcf.gz -c repo_utils/test_files/variants/bnd.comp.vcf.gz -p 0 -o test_results/bench_bnd/ --no-decompose
+2025-01-08 20:16:32,129 [INFO] Params:
 {
     "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",
@@ -35,33 +35,36 @@
     "short_circuit": false,
     "skip_gt": false
 }
-2025-01-08 19:03:15,294 [WARNING] 193 contigs present in comparison VCF header are not in baseline VCF.
-2025-01-08 19:03:15,364 [INFO] Zipped 418 variants Counter({'comp': 243, 'base': 175})
-2025-01-08 19:03:15,365 [INFO] 185 chunks of 418 variants Counter({'comp': 190, '__filtered': 115, 'base': 113})
-2025-01-08 19:03:15,412 [INFO] Stats: {
-    "TP-base": 85,
-    "TP-comp": 85,
-    "FP": 81,
-    "FN": 28,
-    "precision": 0.5120481927710844,
-    "recall": 0.7522123893805309,
-    "f1": 0.6093189964157706,
-    "base cnt": 113,
-    "comp cnt": 166,
-    "TP-comp_TP-gt": 68,
-    "TP-comp_FP-gt": 17,
-    "TP-base_TP-gt": 68,
-    "TP-base_FP-gt": 17,
+2025-01-08 20:16:32,143 [WARNING] 193 contigs present in comparison VCF header are not in baseline VCF.
+2025-01-08 20:16:32,220 [INFO] Zipped 439 variants Counter({'comp': 243, 'base': 196})
+2025-01-08 20:16:32,220 [INFO] 202 chunks of 439 variants Counter({'comp': 190, 'base': 135, '__filtered': 114})
+2025-01-08 20:16:32,268 [INFO] Stats: {
+    "TP-base": 80,
+    "TP-comp": 80,
+    "FP": 88,
+    "FN": 55,
+    "precision": 0.47619047619047616,
+    "recall": 0.5925925925925926,
+    "f1": 0.528052805280528,
+    "base cnt": 135,
+    "comp cnt": 168,
+    "TP-comp_TP-gt": 64,
+    "TP-comp_FP-gt": 16,
+    "TP-base_TP-gt": 64,
+    "TP-base_FP-gt": 16,
     "gt_concordance": 0.8,
     "gt_matrix": {
         "(0, 1)": {
-            "(0, 1)": 65,
-            "(0, 0)": 16,
+            "(0, 1)": 59,
+            "(0, 0)": 15,
             "(1, 1)": 1
         },
         "(1, 0)": {
             "(0, 1)": 3
+        },
+        "(0, 0, 1)": {
+            "(0, 1)": 2
         }
     }
 }
-2025-01-08 19:03:15,412 [INFO] Finished bench
+2025-01-08 20:16:32,268 [INFO] Finished bench

repo_utils/answer_key/bench/bench_bnd/summary.json

@@ -1,26 +1,29 @@
 {
-    "TP-base": 85,
-    "TP-comp": 85,
-    "FP": 81,
-    "FN": 28,
-    "precision": 0.5120481927710844,
-    "recall": 0.7522123893805309,
-    "f1": 0.6093189964157706,
-    "base cnt": 113,
-    "comp cnt": 166,
-    "TP-comp_TP-gt": 68,
-    "TP-comp_FP-gt": 17,
-    "TP-base_TP-gt": 68,
-    "TP-base_FP-gt": 17,
+    "TP-base": 80,
+    "TP-comp": 80,
+    "FP": 88,
+    "FN": 55,
+    "precision": 0.47619047619047616,
+    "recall": 0.5925925925925926,
+    "f1": 0.528052805280528,
+    "base cnt": 135,
+    "comp cnt": 168,
+    "TP-comp_TP-gt": 64,
+    "TP-comp_FP-gt": 16,
+    "TP-base_TP-gt": 64,
+    "TP-base_FP-gt": 16,
     "gt_concordance": 0.8,
     "gt_matrix": {
         "(0, 1)": {
-            "(0, 1)": 65,
-            "(0, 0)": 16,
+            "(0, 1)": 59,
+            "(0, 0)": 15,
             "(1, 1)": 1
         },
         "(1, 0)": {
             "(0, 1)": 3
+        },
+        "(0, 0, 1)": {
+            "(0, 1)": 2
         }
     }
 }

repo_utils/answer_key/bench/bench_bnd_decomp/candidate.refine.bed

@@ -8343,7 +8343,7 @@ chr17	31964205	32004139
 chr17	32092175	32092252
 chr17	32109708	32110047
 chr17	32276768	32276789
-chr17	32305433	32677822
+chr17	32305434	32677819
 chr17	32948020	32948041
 chr17	33357020	33357041
 chr17	33464495	33464582
@@ -9510,7 +9510,7 @@ chr19	9970026	9970047
 chr19	10377655	10377676
 chr19	10714997	10715018
 chr19	10758333	10758354
-chr19	11196126	11219734
+chr19	11196126	11219071
 chr19	11613135	11613156
 chr19	11811887	11811991
 chr19	12365158	12365179
@@ -16472,7 +16472,7 @@ chr7	68462829	68462850
 chr7	68535131	68535152
 chr7	68664068	68664222
 chr7	68761501	68761522
-chr7	68922678	68950323
+chr7	68949177	68949198
 chr7	68959651	68959672
 chr7	68997073	68997413
 chr7	69027642	69027663

repo_utils/answer_key/bench/bench_bnd_decomp/log.txt

@@ -1,6 +1,6 @@
-2025-01-08 18:56:46,711 [INFO] Truvari v5.0.0
-2025-01-08 18:56:46,711 [INFO] Command /Users/english/code/truvari/truvari/__main__.py bench -b repo_utils/test_files/variants/bnd.base.vcf.gz -c repo_utils/test_files/variants/bnd.comp2.vcf.gz --sizemax 1000000000 -p 0 --pick multi -o test_results/bench_bnd_decomp/
-2025-01-08 18:56:46,711 [INFO] Params:
+2025-01-08 20:17:40,376 [INFO] Truvari v5.0.0
+2025-01-08 20:17:40,377 [INFO] Command /Users/english/code/truvari/truvari/__main__.py bench -b repo_utils/test_files/variants/bnd.base.vcf.gz -c repo_utils/test_files/variants/bnd.comp2.vcf.gz --sizemax 1000000000 -p 0 --pick multi -o test_results/bench_bnd_decomp/
+2025-01-08 20:17:40,377 [INFO] Params:
 {
     "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.comp2.vcf.gz",
@@ -35,32 +35,47 @@
     "short_circuit": false,
     "skip_gt": false
 }
-2025-01-08 18:56:46,741 [WARNING] 193 contigs present in comparison VCF header are not in baseline VCF.
-2025-01-08 18:56:52,141 [INFO] Zipped 30077 variants Counter({'comp': 29902, 'base': 175})
-2025-01-08 18:56:52,141 [INFO] 20652 chunks of 30077 variants Counter({'comp': 29902, 'base': 170, '__filtered': 5})
-2025-01-08 18:56:55,373 [INFO] Stats: {
-    "TP-base": 137,
-    "TP-comp": 129,
-    "FP": 28401,
-    "FN": 33,
-    "precision": 0.00452155625657203,
-    "recall": 0.8058823529411765,
-    "f1": 0.0089926574974431,
-    "base cnt": 170,
+2025-01-08 20:17:40,408 [WARNING] 193 contigs present in comparison VCF header are not in baseline VCF.
+2025-01-08 20:17:45,964 [INFO] Zipped 30098 variants Counter({'comp': 29902, 'base': 196})
+2025-01-08 20:17:45,965 [INFO] 20659 chunks of 30098 variants Counter({'comp': 29902, 'base': 186, '__filtered': 10})
+2025-01-08 20:17:49,303 [INFO] Stats: {
+    "TP-base": 144,
+    "TP-comp": 126,
+    "FP": 28404,
+    "FN": 42,
+    "precision": 0.004416403785488959,
+    "recall": 0.7741935483870968,
+    "f1": 0.008782706432809682,
+    "base cnt": 186,
     "comp cnt": 28530,
     "TP-comp_TP-gt": 1,
-    "TP-comp_FP-gt": 128,
+    "TP-comp_FP-gt": 125,
     "TP-base_TP-gt": 1,
-    "TP-base_FP-gt": 136,
-    "gt_concordance": 0.007751937984496124,
+    "TP-base_FP-gt": 143,
+    "gt_concordance": 0.007936507936507936,
     "gt_matrix": {
         "(0, 1)": {
-            "(0, 0)": 134,
+            "(0, 0)": 132,
             "(0, 1)": 1
         },
+        "(0, 0, 1)": {
+            "(0, 0)": 3
+        },
+        "(0, 1, 0)": {
+            "(0, 0)": 2
+        },
+        "(0, 0, 0, 1)": {
+            "(0, 0)": 1
+        },
+        "(0, 0, 1, 0)": {
+            "(0, 0)": 1
+        },
+        "(0, 1, 1)": {
+            "(0, 0)": 2
+        },
         "(1, 0)": {
             "(0, 0)": 2
         }
     }
 }
-2025-01-08 18:56:55,373 [INFO] Finished bench
+2025-01-08 20:17:49,303 [INFO] Finished bench

repo_utils/answer_key/bench/bench_bnd_decomp/summary.json

@@ -1,23 +1,38 @@
 {
-    "TP-base": 137,
-    "TP-comp": 129,
-    "FP": 28401,
-    "FN": 33,
-    "precision": 0.00452155625657203,
-    "recall": 0.8058823529411765,
-    "f1": 0.0089926574974431,
-    "base cnt": 170,
+    "TP-base": 144,
+    "TP-comp": 126,
+    "FP": 28404,
+    "FN": 42,
+    "precision": 0.004416403785488959,
+    "recall": 0.7741935483870968,
+    "f1": 0.008782706432809682,
+    "base cnt": 186,
     "comp cnt": 28530,
     "TP-comp_TP-gt": 1,
-    "TP-comp_FP-gt": 128,
+    "TP-comp_FP-gt": 125,
     "TP-base_TP-gt": 1,
-    "TP-base_FP-gt": 136,
-    "gt_concordance": 0.007751937984496124,
+    "TP-base_FP-gt": 143,
+    "gt_concordance": 0.007936507936507936,
     "gt_matrix": {
         "(0, 1)": {
-            "(0, 0)": 134,
+            "(0, 0)": 132,
             "(0, 1)": 1
         },
+        "(0, 0, 1)": {
+            "(0, 0)": 3
+        },
+        "(0, 1, 0)": {
+            "(0, 0)": 2
+        },
+        "(0, 0, 0, 1)": {
+            "(0, 0)": 1
+        },
+        "(0, 0, 1, 0)": {
+            "(0, 0)": 1
+        },
+        "(0, 1, 1)": {
+            "(0, 0)": 2
+        },
         "(1, 0)": {
             "(0, 0)": 2
         }

repo_utils/sub_tests/bench.sh

@@ -75,7 +75,7 @@ run bench_gtcomp_edgecase1 $truv bench -b $INDIR/variants/gtcomp_problem1_base.v
 if [ $bench_gtcomp_edgecase1 ]; then
     bench_assert _gtcomp_edgecase1
 fi
-run bench_badparams $truv bench -b nofile.vcf -c nofile.aga -f notref.fa -o $OD --refdist 0 --extend
+run bench_badparams $truv bench -b nofile.vcf -c nofile.aga -f notref.fa -o $OD --refdist 0 --extend 1
 if [ $bench_badparams ]; then
     assert_exit_code 100
 fi

truvari/variant_record.py

@@ -119,7 +119,7 @@ def bnd_position(self):
         """
         Extracts the chromosome and position from a BND ALT string.
 
-        Breakend (BND) ALT strings indicate structural variant breakpoints that span across chromosomes or positions. 
+        Breakend (BND) ALT strings indicate structural variant breakpoints that span across chromosomes or positions.
         This method parses the ALT string to extract the target chromosome and position of the breakpoint.
 
         :return: A tuple containing the chromosome (as a string) and the position (as an integer).
@@ -298,11 +298,13 @@ def decompose(self):
             raise ValueError("Can only decompose symbolic variants")
         if self.decomp_repr:
             return self.decomp_repr
+
         svtype = self.var_type()
         chrom = self.chrom
         pos = self.pos
         end = self.end
         ret = []
+
         if svtype == truvari.SV.INV:
             record1 = self.copy()
             record1.alts = (f"[{chrom}:{end}[N",)
@@ -338,15 +340,16 @@ def decompose(self):
 
         elif svtype == truvari.SV.DUP:
             record1 = self.copy()
-            record1.alts = (f"N]chr{chrom}:{end}]",)
-            record1.info["SVTYPE"] = "BND"
+            record1.alts = (f"]{chrom}:{end}]N",)
+            record1.info["SVTYPE"] == "BND"
 
             record2 = self.copy()
             record2.pos = end
-            record2.alts = (f"[chr{chrom}:{pos}[N",)
+            record2.alts = (f"N[{chrom}:{pos}[",)
             record2.info["SVTYPE"] = "BND"
 
             ret = [record1, record2]
+
         self.decomp_repr = ret
         return ret