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Bugfix for IndelLengthHistogram 

-- Wasn't requiring the allele to actually be polymorphic in the samples, so it wasn't working correctly with the Sample strat.
This commit is contained in:
Mark DePristo 2012-04-04 14:28:49 -04:00
parent 3593996a87
commit fcdd65a0f4
1 changed files with 7 additions and 4 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
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@ -85,10 +85,13 @@ public class IndelLengthHistogram extends VariantEvaluator implements StandardEv
@Override
public void update1(final VariantContext eval, final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
if ( eval.isIndel() && ! eval.isComplexIndel() ) {
for ( Allele alt : eval.getAlternateAlleles() ) {
final int alleleSize = alt.length() - eval.getReference().length();
if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
updateLengthHistogram(eval.getReference(), alt);
if ( ! ( getWalker().ignoreAC0Sites() && eval.isMonomorphicInSamples() )) {
// only if we are actually polymorphic in the subsetted samples should we count the allele
for ( Allele alt : eval.getAlternateAlleles() ) {
final int alleleSize = alt.length() - eval.getReference().length();
if ( alleleSize == 0 ) throw new ReviewedStingException("Allele size not expected to be zero for indel: alt = " + alt + " ref = " + eval.getReference());
updateLengthHistogram(eval.getReference(), alt);
}
}
}
}