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Fix for bug reported on GetSatisfaction

This commit is contained in:
Eric Banks 2011-11-09 20:33:36 -05:00
parent d00b2c6599
commit 04b122be29
1 changed files with 2 additions and 0 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
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@ -59,6 +59,8 @@ public class BaseCounts extends InfoFieldAnnotation {
int[] counts = new int[4]; int[] counts = new int[4];
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) { for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
if ( !sample.getValue().hasBasePileup() )
continue;
for (byte base : sample.getValue().getBasePileup().getBases() ) { for (byte base : sample.getValue().getBasePileup().getBases() ) {
int index = BaseUtils.simpleBaseToBaseIndex(base); int index = BaseUtils.simpleBaseToBaseIndex(base);
if ( index != -1 ) if ( index != -1 )