zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix possible null pointer exception 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3666 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-29 09:01:18 +00:00
parent 2953c9f069
commit 929e5b9276
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
View File

@ -171,7 +171,7 @@ 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().size() == 0 ) else if ( hasIndel && (context.getBasePileup() == null || context.getBasePileup().size() == 0) )
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);