From c1abcfb0144ed3f6910dec576a593c3f36c4d020 Mon Sep 17 00:00:00 2001 From: depristo Date: Fri, 3 Apr 2009 19:53:33 +0000 Subject: [PATCH] Fixed problem where we were considering reads out of order because their stop positions where out of order, but with equal starts. This involved a change in the ordering feature of GenomeLoc, which now no longer sorts by both start and stop. So as long as the start positions are equal, things are considered "in order". Perhaps this isn't a good idea to change... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@291 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index a7a49ff48..ad1b2381b 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -475,8 +475,11 @@ public class GenomeLoc implements Comparable { if ( cmpContig != 0 ) return cmpContig; if ( this.getStart() < that.getStart() ) return -1; if ( this.getStart() > that.getStart() ) return 1; - if ( this.getStop() < that.getStop() ) return -1; - if ( this.getStop() > that.getStop() ) return 1; + + // TODO: and error is being thrown because we are treating reads with the same start positions + // but different stop as out of order + //if ( this.getStop() < that.getStop() ) return -1; + //if ( this.getStop() > that.getStop() ) return 1; return 0; } }