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Reduced reads shouldn't contribute to Fisher Strand calculations

This commit is contained in:
Eric Banks 2011-11-02 13:07:20 -04:00
parent cf0e699226
commit 967ff647b8
1 changed files with 3 additions and 1 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -205,7 +205,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
for (PileupElement p : sample.getValue().getBasePileup()) {
if ( p.isDeletion() ) // ignore deletions
if ( p.isDeletion() || p.isReducedRead() ) // ignore deletions and reduced reads
continue;
if ( p.getRead().getMappingQuality() < 20 || p.getQual() < 20 )
@ -258,6 +258,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
continue;
for (final PileupElement p: pileup) {
if ( p.isReducedRead() ) // ignore reduced reads
continue;
if ( p.getRead().getMappingQuality() < 20)
continue;
if (indelLikelihoodMap.containsKey(p)) {