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Check for bad intervals and don't emit them 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2849 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-02-16 21:42:36 +00:00
parent f859e14cc7
commit 2520889cb3
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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@ -214,7 +214,7 @@ public class RealignerTargetCreator extends LocusWalker<RealignerTargetCreator.E
}
public boolean isReportableEvent() {
return eventStartPos >= 0 && eventStopPos >= 0 && eventStopPos - eventStartPos < maxIntervalSize;
return GenomeLocParser.validGenomeLoc(loc.getContig(), eventStartPos, eventStopPos) && eventStopPos >= 0 && eventStopPos - eventStartPos < maxIntervalSize;
}
public String toString() {