From 9bd8a2685b5938c135c57932acb9a4cbf21d3f00 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 25 Jul 2010 02:53:01 +0000
Subject: [PATCH] Because the performance tests were busted on LSF, no one
 caught this error until now: when Matt changed over the contract for the
 AlignmentContext, this line needed to get updated too.  All is well now.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3873 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/RealignerTargetCreator.java       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index c0f2c90ea..0e958fc01 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -172,7 +172,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
         GenomeLoc eventLoc = context.getLocation();
         if ( hasInsertion )
             eventLoc =  GenomeLocParser.createGenomeLoc(eventLoc.getContigIndex(), eventLoc.getStart(), eventLoc.getStart()+1);
-        else if ( hasIndel && (context.getBasePileup() == null || context.getBasePileup().size() == 0) )
+        else if ( hasIndel && !context.hasBasePileup() )
             eventLoc =  GenomeLocParser.createGenomeLoc(eventLoc.getContigIndex(), eventLoc.getStart(), furthestStopPos);        
 
         EVENT_TYPE eventType = (hasIndel ? (hasPointEvent ? EVENT_TYPE.BOTH : EVENT_TYPE.INDEL_EVENT) : EVENT_TYPE.POINT_EVENT);