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Fix possible NPE from NBaseCount annotation module

This commit is contained in:
Eric Banks 2012-05-29 09:46:00 -04:00
parent 08de4dfd96
commit 50031b63c5
1 changed files with 2 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
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@ -30,7 +30,8 @@ public class NBaseCount extends InfoFieldAnnotation {
for( final AlignmentContext context : stratifiedContexts.values() ) {
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") ) {
final String platform = p.getRead().getReadGroup().getPlatform();
if( platform != null && platform.toUpperCase().contains("SOLID") ) {
if( BaseUtils.isNBase( p.getBase() ) ) {
countNBaseSolid++;
} else if( BaseUtils.isRegularBase( p.getBase() ) ) {