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Ask for existance of extended pileup before grabbing it 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5874 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2011-05-25 17:39:03 +00:00
parent 9d8c963fcc
commit bafdd4f8f7
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -82,7 +82,7 @@ public class AlleleBalance implements InfoFieldAnnotation {
// weight the allele balance by genotype quality so that e.g. mis-called homs don't affect the ratio too much // weight the allele balance by genotype quality so that e.g. mis-called homs don't affect the ratio too much
ratio += genotype.getValue().getNegLog10PError() * ((double)refCount / (double)(refCount + altCount)); ratio += genotype.getValue().getNegLog10PError() * ((double)refCount / (double)(refCount + altCount));
totalWeights += genotype.getValue().getNegLog10PError(); totalWeights += genotype.getValue().getNegLog10PError();
} else if ( vc.isIndel() ) { } else if ( vc.isIndel() && context.hasExtendedEventPileup() ) {
final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup(); final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
if ( indelPileup == null ) { if ( indelPileup == null ) {
continue; continue;