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Remove filtering of MAPQ 0 reads from CalledHaplotypeBAMWriter

This commit is contained in:
Mark DePristo 2013-07-01 14:55:15 -04:00
parent 7be01777f6
commit 5f34054cc1
1 changed files with 2 additions and 4 deletions
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2
protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
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@ -98,11 +98,9 @@ class CalledHaplotypeBAMWriter extends HaplotypeBAMWriter {
// next, output the interesting reads for each sample aligned against one of the called haplotypes // next, output the interesting reads for each sample aligned against one of the called haplotypes
for ( final PerReadAlleleLikelihoodMap readAlleleLikelihoodMap : stratifiedReadMap.values() ) { for ( final PerReadAlleleLikelihoodMap readAlleleLikelihoodMap : stratifiedReadMap.values() ) {
for ( final Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : readAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) { for ( final Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : readAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) {
if ( entry.getKey().getMappingQuality() > 0 ) {
final MostLikelyAllele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue(), allelesOfCalledHaplotypes); final MostLikelyAllele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue(), allelesOfCalledHaplotypes);
writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele()), paddedReferenceLoc.getStart(), bestAllele.isInformative()); writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele()), paddedReferenceLoc.getStart(), bestAllele.isInformative());
} }
} }
} }
}
} }