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Fixed bug that failed to reset an accumulator when crossing contig boundaries, 

meaning that in special cases of shallow coverage, an interval might get dropped.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2999 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-15 04:45:55 +00:00
parent 73d6167bd6
commit 45f70de6df
1 changed files with 6 additions and 0 deletions
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6
java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
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@ -24,6 +24,12 @@ public class IntervalSharder {
FilePointer filePointer = null;
for(GenomeLoc location: loci) {
// If crossing contigs, be sure to reset the filepointer that's been accumulating shard data.
if(filePointer != null && filePointer.bin.referenceSequence != location.getContigIndex()) {
filePointers.add(filePointer);
filePointer = null;
}
int locationStart = (int)location.getStart();
final int locationStop = (int)location.getStop();