diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java index 04ab385f16c..28cd0c9a7af 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/varianteval/evaluators/MendelianViolationEvaluator.java @@ -142,7 +142,7 @@ public void update1(final VariantContext vc, final VariantEvalContext context) { HomVarHet_inheritedRef += mv.getParentsVarHetInheritedRef(); HomVarHet_inheritedVar += mv.getParentsVarHetInheritedVar(); - if(mv.getFamilyCalledCount()>0 || mv.getFamilyLowQualsCount()>0 || mv.getFamilyCalledCount()>0){ + if(mv.getFamilyCalledCount()>0 || mv.getFamilyLowQualsCount()>0 || mv.getFamilyNoCallCount()>0){ nVariants++; nFamCalled += mv.getFamilyCalledCount(); nLowQual += mv.getFamilyLowQualsCount(); @@ -155,7 +155,7 @@ public void update1(final VariantContext vc, final VariantEvalContext context) { } } - private class ExtendedMendelianViolation extends MendelianViolation + private static class ExtendedMendelianViolation extends MendelianViolation { public ExtendedMendelianViolation(double threshold) {