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Don't penalize the reduced reads for spanning deletions (when surrounding base quals are Q2s)

This commit is contained in:
Eric Banks 2012-09-24 14:06:07 -04:00
parent 6a73265a06
commit 9464dfdbf2
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java
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@ -99,7 +99,7 @@ public class AssessReducedCoverage extends LocusWalker<GenomeLoc, GenomeLoc> imp
final Set<String> tags = new HashSet<String>(10); final Set<String> tags = new HashSet<String>(10);
for ( final PileupElement p : pileup ) { for ( final PileupElement p : pileup ) {
if ( (int)p.getQual() > 2 && p.getMappingQual() > 0 ) if ( (int)p.getQual() > 2 && p.getMappingQual() > 0 && !p.isDeletion() )
tags.addAll(getToolkit().getReaderIDForRead(p.getRead()).getTags().getPositionalTags()); tags.addAll(getToolkit().getReaderIDForRead(p.getRead()).getTags().getPositionalTags());
} }