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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
This commit is contained in:
ebanks 2010-07-25 02:53:01 +00:00
parent b551eaf8fd
commit 9bd8a2685b
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -172,7 +172,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
GenomeLoc eventLoc = context.getLocation(); GenomeLoc eventLoc = context.getLocation();
if ( hasInsertion ) if ( hasInsertion )
eventLoc = GenomeLocParser.createGenomeLoc(eventLoc.getContigIndex(), eventLoc.getStart(), eventLoc.getStart()+1); 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); eventLoc = GenomeLocParser.createGenomeLoc(eventLoc.getContigIndex(), eventLoc.getStart(), furthestStopPos);
EVENT_TYPE eventType = (hasIndel ? (hasPointEvent ? EVENT_TYPE.BOTH : EVENT_TYPE.INDEL_EVENT) : EVENT_TYPE.POINT_EVENT); EVENT_TYPE eventType = (hasIndel ? (hasPointEvent ? EVENT_TYPE.BOTH : EVENT_TYPE.INDEL_EVENT) : EVENT_TYPE.POINT_EVENT);