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Avoid calling getBasePileup when there's no pileup in NBaseCount annotation

This commit is contained in:
Mark DePristo 2012-02-27 15:12:25 -05:00
parent 729bb954e2
commit 5f7ccdcc01
1 changed files with 9 additions and 7 deletions
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16
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
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@ -27,13 +27,15 @@ public class NBaseCount extends InfoFieldAnnotation {
int countNBaseSolid = 0; int countNBaseSolid = 0;
int countRegularBaseSolid = 0; int countRegularBaseSolid = 0;
for( final Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) { for( final AlignmentContext context : stratifiedContexts.values() ) {
for( final PileupElement p : sample.getValue().getBasePileup()) { if ( context.hasBasePileup() ) { // must be called as getBasePileup may throw error when pileup has no bases
if( p.getRead().getReadGroup().getPlatform().toUpperCase().contains("SOLID") ) { for( final PileupElement p : context.getBasePileup()) {
if( BaseUtils.isNBase( p.getBase() ) ) { if( p.getRead().getReadGroup().getPlatform().toUpperCase().contains("SOLID") ) {
countNBaseSolid++; if( BaseUtils.isNBase( p.getBase() ) ) {
} else if( BaseUtils.isRegularBase( p.getBase() ) ) { countNBaseSolid++;
countRegularBaseSolid++; } else if( BaseUtils.isRegularBase( p.getBase() ) ) {
countRegularBaseSolid++;
}
} }
} }
} }