zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
This commit is contained in:
depristo 2009-04-03 19:53:33 +00:00
parent ef06924f73
commit c1abcfb014
1 changed files with 5 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
View File

@ -475,8 +475,11 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
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;
}
}