From 22d1e6323b3bac1e2c26e32cc85022ce69976db5 Mon Sep 17 00:00:00 2001 From: bartcharbon Date: Thu, 17 Feb 2022 10:18:37 +0100 Subject: [PATCH] Fix nullpointer in ArCompoundChecker --- .../vcf/inheritance/matcher/checker/ArCompoundChecker.java | 3 +++ src/test/resources/ArCompoundTests.tsv | 1 + src/test/resources/pedigree_complex.ped | 3 ++- 3 files changed, 6 insertions(+), 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 index 6e80112..e22ac79 100644 --- 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 index f9da726..55bc8a7 100644 --- 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 index 4d369f2..211da68 100644 --- 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 \ No newline at end of file