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Check for a reference before extraction. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@661 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-12 13:29:44 +00:00
parent 32696b13f5
commit 608948210c
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -106,7 +106,8 @@ public class TraverseReads extends TraversalEngine {
locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0)); locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0));
// get the array of characters for the reference sequence, since we're a mapped read // get the array of characters for the reference sequence, since we're a mapped read
refSeq = dataProvider.getReferenceForRead( read ); if( dataProvider.hasReference() )
refSeq = dataProvider.getReferenceForRead( read );
} }
// update the number of reads we've seen // update the number of reads we've seen