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More comprehensive support when sharding for ref walkers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2951 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-08 11:25:20 +00:00
parent eb165ca844
commit e4360bac6a
1 changed files with 8 additions and 3 deletions
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11
java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
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@ -95,10 +95,15 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
filePointers.addAll(IntervalSharder.shardIntervals(this.reads,intervals,this.reads.getNumIndexLevels()-1)); filePointers.addAll(IntervalSharder.shardIntervals(this.reads,intervals,this.reads.getNumIndexLevels()-1));
} }
else { else {
// TODO: Non-intervaled ref traversals.
this.reads = null; this.reads = null;
for(GenomeLoc interval: locations) if(locations == null) {
filePointers.add(new FilePointer(interval)); for(SAMSequenceRecord refSequenceRecord: reference.getSequenceDictionary().getSequences())
filePointers.add(new FilePointer(GenomeLocParser.createGenomeLoc(refSequenceRecord.getSequenceName(),1,refSequenceRecord.getSequenceLength())));
}
else {
for(GenomeLoc interval: locations)
filePointers.add(new FilePointer(interval));
}
} }
filePointerIterator = filePointers.iterator(); filePointerIterator = filePointers.iterator();