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

quietly skip empty intervals files rather than crash. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1428 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-08-17 20:19:14 +00:00
parent 92c63fb530
commit 1e8b97b560
1 changed files with 13 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
View File

@ -33,6 +33,9 @@ import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
import java.util.*; import java.util.*;
import java.io.*;
/** /**
* Merges intervals based on reads which overlap them. * Merges intervals based on reads which overlap them.
*/ */
@ -111,6 +114,15 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
* @return a linked list of sorted, merged intervals. * @return a linked list of sorted, merged intervals.
*/ */
private LinkedList<GenomeLoc> parseIntervals(List<String> intervalsSource) { private LinkedList<GenomeLoc> parseIntervals(List<String> intervalsSource) {
// ignore zero-length intervals files.
for (int i = 0; i < intervalsSource.size(); i++)
{
File f = new File(intervalsSource.get(i));
long size = f.length();
if (size == 0) { intervalsSource.remove(i); }
}
List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource); List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource);
GenomeLocSortedSet intervalSortedSet = new GenomeLocSortedSet(); GenomeLocSortedSet intervalSortedSet = new GenomeLocSortedSet();
for ( GenomeLoc parsedInterval : parsedIntervals ) for ( GenomeLoc parsedInterval : parsedIntervals )
@ -118,4 +130,4 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
return new LinkedList<GenomeLoc>( intervalSortedSet ); return new LinkedList<GenomeLoc>( intervalSortedSet );
} }
} }