From bafdd4f8f79623e583032f428ed0f22cb00b5681 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 May 2011 17:39:03 +0000
Subject: [PATCH] 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
---
 .../sting/gatk/walkers/annotator/AlleleBalance.java             | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index d3beb64aa..9b3ec0f74 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -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
                 ratio += genotype.getValue().getNegLog10PError() * ((double)refCount / (double)(refCount + altCount));
                 totalWeights += genotype.getValue().getNegLog10PError();
-            } else if ( vc.isIndel() ) {
+            } else if ( vc.isIndel() && context.hasExtendedEventPileup() ) {
                 final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
                 if ( indelPileup == null ) {
                     continue;