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Better error message for unused ALT alleles

This commit is contained in:
Eric Banks 2012-10-29 21:51:35 -04:00
parent b6a1967f12
commit c95e893920
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -1073,13 +1073,13 @@ public class VariantContext implements Feature { // to enable tribble integratio
} }
if ( reportedAlleles.size() != observedAlleles.size() ) if ( reportedAlleles.size() != observedAlleles.size() )
throw new TribbleException.InternalCodecException(String.format("the ALT allele(s) for the record at position %s:%d do not match what is observed in the per-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()));
int originalSize = reportedAlleles.size(); int originalSize = reportedAlleles.size();
// take the intersection and see if things change // take the intersection and see if things change
observedAlleles.retainAll(reportedAlleles); observedAlleles.retainAll(reportedAlleles);
if ( observedAlleles.size() != originalSize ) if ( observedAlleles.size() != originalSize )
throw new TribbleException.InternalCodecException(String.format("the ALT allele(s) for the record at position %s:%d do not match what is observed in the per-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()));
} }
public void validateChromosomeCounts() { public void validateChromosomeCounts() {