From 80cbc1924b0885d66c5f60e8ef749a88a4ddd82e Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 3 Jun 2011 18:06:41 +0000 Subject: [PATCH] Oops, just realized that I forgot to comment my commit from yesterday so it was clear what was happening git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5938 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/utils/GenomeLocParser.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index 7f22f7294..18a1e7ffd 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -435,7 +435,7 @@ public class GenomeLocParser { // read is unmapped and not placed anywhere on the genome return GenomeLoc.UNMAPPED; else { - // + // Use Math.max to ensure that end >= start (Picard assigns the end to reads that are entirely within an insertion as start-1) int end = read.getReadUnmappedFlag() ? read.getAlignmentStart() : Math.max(read.getAlignmentEnd(), read.getAlignmentStart()); return createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getAlignmentStart(), end, false); }