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

Eliminate a few stray loci that weren't being filtered out. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2875 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-02-23 18:00:52 +00:00
parent fff15944fe
commit 491b30e8de
1 changed files with 1 additions and 19 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
View File

@ -157,29 +157,11 @@ public abstract class LocusView extends LocusIterator implements View {
nextLocus = loci.next();
// If nothing in the shard was found, indicate that by setting nextAlignmentContext to null.
if( nextLocus != null && (isBeforeShard(nextLocus.getLocation()) || isAfterShard(nextLocus.getLocation())) )
if( nextLocus != null && !isContainedInShard(nextLocus.getLocation()) )
nextLocus = null;
}
}
/**
* Is this location before the given shard.
* @param location Location to check.
* @return True if the given location is before the start of the shard. False otherwise.
*/
private boolean isBeforeShard(GenomeLoc location) {
return location.isBefore(shard.getGenomeLocs().get(0));
}
/**
* Is this location after the given shard.
* @param location Location to check.
* @return True if the given location is after the end of the shard. False otherwise.
*/
private boolean isAfterShard(GenomeLoc location) {
return location.isPast(shard.getGenomeLocs().get(shard.getGenomeLocs().size()-1));
}
/**
* Is this location contained in the given shard.
* @param location Location to check.