From d0ca6f8a9c187e523b28b9265a52d931d60bb4de Mon Sep 17 00:00:00 2001 From: ebanks Date: Thu, 2 Jun 2011 20:40:56 +0000 Subject: [PATCH] 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 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index 732d52b2b..7f22f7294 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/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); } }