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

java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java

@@ -124,6 +124,10 @@ public class TraverseReads extends TraversalEngine {
                 // get the genome loc from the 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
                 locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0));