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temporary fix to deal with screwy SOLiD reads 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1168 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2009-07-05 03:25:57 +00:00
parent cf1854b339
commit e5e249d4ac
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -124,6 +124,10 @@ public class TraverseReads extends TraversalEngine {
// get the genome loc from the read // get the genome loc from the read
GenomeLoc site = GenomeLocParser.createGenomeLoc(read); GenomeLoc site = GenomeLocParser.createGenomeLoc(read);
// this is a temporary fix to deal with unmapped reads which "map" to a given location and have a MAPPED flag set
if ( site.getStop() != -1 && site.getStop() < site.getStart() )
continue;
// Jump forward in the reference to this locus location // Jump forward in the reference to this locus location
locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0)); locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0));