Update MendelianViolation . Fix java.lang.IndexOutOfBoundsException: when a genotype is haploid.#9241
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lindenb wants to merge 1 commit into
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Update MendelianViolation . Fix java.lang.IndexOutOfBoundsException: when a genotype is haploid.#9241lindenb wants to merge 1 commit into
lindenb wants to merge 1 commit into
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fix MendelianViolation when a sample is haploid
```
java.lang.IndexOutOfBoundsException: Index 1 out of bounds for length 1
at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:64)
at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:70)
at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:266)
at java.base/java.util.Objects.checkIndex(Objects.java:359)
at java.base/java.util.ArrayList.get(ArrayList.java:427)
at org.broadinstitute.hellbender.utils.samples.MendelianViolation.isViolation(MendelianViolation.java:180)
at org.broadinstitute.hellbender.utils.samples.MendelianViolation.updateViolations(MendelianViolation.java:122)
at org.broadinstitute.hellbender.utils.samples.MendelianViolation.isViolation(MendelianViolation.java:81)
at org.broadinstitute.hellbender.tools.walkers.annotator.PossibleDeNovo.annotate(PossibleDeNovo.java:119)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.addInfoAnnotations(VariantAnnotatorEngine.java:394)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:367)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngine.annotateContext(VariantAnnotatorEngine.java:338)
at org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator.apply(VariantAnnotator.java:243)
at org.broadinstitute.hellbender.engine.VariantWalker.lambda$traverse$0(VariantWalker.java:104)
at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179)
at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
```
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Hi the GATK team,
this PR fiesx a bug in MendelianViolation when a sample is haploid.
sorry, not tested: I'm currently editing the code using the github interface.