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Bug fix: don't add no-call alleles to the list of ALT alleles being validated.

This commit is contained in:
Eric Banks 2012-10-30 14:54:29 -04:00
parent 2aa28abe0a
commit e1e480a0b9
1 changed files with 2 additions and 0 deletions
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2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -1071,6 +1071,8 @@ public class VariantContext implements Feature { // to enable tribble integratio
if ( g.isCalled() ) if ( g.isCalled() )
observedAlleles.addAll(g.getAlleles()); observedAlleles.addAll(g.getAlleles());
} }
if ( observedAlleles.contains(Allele.NO_CALL) )
observedAlleles.remove(Allele.NO_CALL);
if ( reportedAlleles.size() != observedAlleles.size() ) if ( reportedAlleles.size() != observedAlleles.size() )
throw new TribbleException.InternalCodecException(String.format("one or more of the ALT allele(s) for the record at position %s:%d are not observed at all in the sample genotypes", getChr(), getStart())); throw new TribbleException.InternalCodecException(String.format("one or more of the ALT allele(s) for the record at position %s:%d are not observed at all in the sample genotypes", getChr(), getStart()));