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Make sure that reference view holds enough bases to pass full-length deleted sequence to the walker's map() function in extended event mode (this addresses the problem of a deletion crossing the shard's boundary, so that an attempt to extract deleted bases results in a crash) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2543 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-01-07 22:37:22 +00:00
parent e9bc85c188
commit d01bde36a4
1 changed files with 6 additions and 0 deletions
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6
java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
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@ -78,6 +78,12 @@ public class TraverseLoci extends TraversalEngine {
// associated with the current site), we need to update the location. The updated location still starts // associated with the current site), we need to update the location. The updated location still starts
// at the current genomic position, but it has to span the length of the longest deletion (if any). // at the current genomic position, but it has to span the length of the longest deletion (if any).
location = GenomeLocParser.setStop(location,location.getStop()+locus.getExtendedEventPileup().getMaxDeletionLength()); location = GenomeLocParser.setStop(location,location.getStop()+locus.getExtendedEventPileup().getMaxDeletionLength());
// it is possible that the new expanded location spans the current shard boundary; the next method ensures
// that when it is the case, the reference sequence held by the ReferenceView will be reloaded so that
// the view has all the bases we are gonna need. If the location fits within the current view bounds,
// the next call will not do anything to the view:
referenceView.expandBoundsToAccomodateLoc(location);
} }
// Iterate forward to get all reference ordered data covering this location // Iterate forward to get all reference ordered data covering this location