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Don't try to create a GenomeLoc from an unmapped read 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5480 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-03-21 13:46:55 +00:00
parent 96628457cb
commit d9202f2764
1 changed files with 3 additions and 2 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
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@ -183,8 +183,9 @@ public class ConstrainedMateFixingManager {
writeRead(waitingReads.remove()); writeRead(waitingReads.remove());
} }
lastLocFlushed = genomeLocParser.createGenomeLoc(waitingReads.peek()); SAMRecord lastRead = waitingReads.remove();
writeRead(waitingReads.remove()); lastLocFlushed = (lastRead.getReferenceIndex() == -1) ? null : genomeLocParser.createGenomeLoc(lastRead);
writeRead(lastRead);
if ( !tooManyReads ) if ( !tooManyReads )
forMateMatching.clear(); forMateMatching.clear();