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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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6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
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@ -27,8 +27,9 @@ 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
for( final PileupElement p : context.getBasePileup()) {
if( p.getRead().getReadGroup().getPlatform().toUpperCase().contains("SOLID") ) { if( p.getRead().getReadGroup().getPlatform().toUpperCase().contains("SOLID") ) {
if( BaseUtils.isNBase( p.getBase() ) ) { if( BaseUtils.isNBase( p.getBase() ) ) {
countNBaseSolid++; countNBaseSolid++;
@ -38,6 +39,7 @@ public class NBaseCount extends InfoFieldAnnotation {
} }
} }
} }
}
final Map<String, Object> map = new HashMap<String, Object>(); final Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.4f", (double)countNBaseSolid / (double)(countNBaseSolid + countRegularBaseSolid + 1))); map.put(getKeyNames().get(0), String.format("%.4f", (double)countNBaseSolid / (double)(countNBaseSolid + countRegularBaseSolid + 1)));
return map; return map;