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Special case handling of unmapped region in low memory sharder. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5346 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2011-03-01 17:38:30 +00:00
parent dd30ad751a
commit 3c7ae0d1a6
1 changed files with 10 additions and 0 deletions
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10
java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
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@ -34,6 +34,7 @@ import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;
@ -85,6 +86,15 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
nextFilePointer = null;
while(nextFilePointer == null && currentLocus != null) {
// special case handling of the unmapped shard.
if(currentLocus == GenomeLoc.UNMAPPED) {
nextFilePointer = new FilePointer(GenomeLoc.UNMAPPED);
for(SAMReaderID id: dataSource.getReaderIDs())
nextFilePointer.addFileSpans(id,null);
currentLocus = null;
continue;
}
nextFilePointer = new FilePointer(currentLocus.getContig());
int coveredRegionStart = 1;