Patch for case that a read spans only an insertion (i.e. no Ms in the CIGAR string): the end position should not be less than the start position (which is how Picard defines it) but instead should be equal to it. This is just a patch; we'll get a proper solution in at some point.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5922 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/GenomeLocParser.java

@@ -435,7 +435,8 @@ public class GenomeLocParser {
             // read is unmapped and not placed anywhere on the genome
             return GenomeLoc.UNMAPPED;
         else {
-            int end = read.getReadUnmappedFlag() ? read.getAlignmentStart() : read.getAlignmentEnd();
+            //
+            int end = read.getReadUnmappedFlag() ? read.getAlignmentStart() : Math.max(read.getAlignmentEnd(), read.getAlignmentStart());
             return createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getAlignmentStart(), end, false);
         }
     }