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ignore uninteresting extended events 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2866 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-02-22 19:55:46 +00:00
parent 32e5dceef9
commit a640bd2d79
1 changed files with 5 additions and 0 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
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@ -114,9 +114,14 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
hasPointEvent = true; hasPointEvent = true;
} }
// return null if no event occurred
if ( !hasIndel && !hasPointEvent ) if ( !hasIndel && !hasPointEvent )
return null; return null;
// return null if we didn't find any usable reads associated with the event
if ( furthestStopPos == -1 )
return null;
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);