Merge pull request #19 from molgenis/fix/compoundCheckNull

Fix #20: ARCompoundChecker throws exception if individual from ped is not in the VCF
molgenis · Feb 18, 2022 · 3608b06 · 3608b06
2 parents 3e35f07 + 22d1e63
commit 3608b06
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Showing 3 changed files with 6 additions and 1 deletion.
diff --git a/src/main/java/org/molgenis/vcf/inheritance/matcher/checker/ArCompoundChecker.java b/src/main/java/org/molgenis/vcf/inheritance/matcher/checker/ArCompoundChecker.java
@@ -80,6 +80,9 @@ private boolean checkIndividual(VariantContext variantContext, VariantContext ot
   }
 
   private boolean checkUnaffectedSample(Genotype sampleGt, Genotype sampleOtherGt) {
+    if(sampleGt == null || sampleOtherGt == null){
+      return true;
+    }
     boolean sampleContainsAlt = !sampleGt.getAlleles().stream()
         .allMatch(allele -> allele.isReference() || allele
             .isNoCall());

diff --git a/src/test/resources/ArCompoundTests.tsv b/src/test/resources/ArCompoundTests.tsv
@@ -1,5 +1,6 @@
 name	probandGt	probandOtherGt	probandAffectedStatus	probandSex	fatherGt	fatherOtherGt	fatherAffectedStatus	motherGt	motherOtherGt	motherAffectedStatus	brotherGt	brotherOtherGt	brotherAffectedStatus	expected
 regular	0/1	0/1	AFFECTED	MALE	0/0	0/1	UNAFFECTED	0/1	0/0	UNAFFECTED				true
+regularBrotherMissingFromVcf	0/1	0/1	AFFECTED	MALE	0/0	0/1	UNAFFECTED	0/1	0/0	UNAFFECTED			UNAFFECTED	true
 regularPhased	1|0	0|1	AFFECTED	MALE	0|0	0|1	UNAFFECTED	0|1	0|0	UNAFFECTED				true
 FatherUnaffectedHasBoth	1/0	0/1	AFFECTED	MALE	0/1	0/1	UNAFFECTED	0/1	0/0	UNAFFECTED				false
 phasedFatherBothSameAllele	1|0	0|1	AFFECTED	MALE	0|1	0|1	UNAFFECTED	0|1	0|0	UNAFFECTED				true

diff --git a/src/test/resources/pedigree_complex.ped b/src/test/resources/pedigree_complex.ped
@@ -1,6 +1,7 @@
 FAM001	Patient	Father	Mother	1	2
 FAM001	Father	0	0	1	1
-FAM001	Mother	0	0	2	1
+FAM001	Mother	0	Mother3	2	1
+FAM001	Mother3	0	0	2	1
 FAM002	Patient2	Father2	0	1	2
 FAM002	Father2	0	0	1	1
 FAM003	Patient3	0	0	1	2