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For parallel ROD traversals, simplified reference sharding. Will replace 

with a more sensible strategy for sharding w/o BAMs at some point after
ASHG.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4549 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-10-22 05:08:15 +00:00
parent 9ba7269728
commit d4feb99d9a
1 changed files with 6 additions and 1 deletions
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7
java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java
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@ -94,8 +94,13 @@ public class LocusShardStrategy implements ShardStrategy {
}
}
else {
for(GenomeLoc interval: locations)
for(GenomeLoc interval: locations) {
while(interval.size() > maxShardSize) {
filePointers.add(new FilePointer(GenomeLocParser.createGenomeLoc(interval.getContig(),interval.getStart(),interval.getStart()+maxShardSize-1)));
interval = GenomeLocParser.createGenomeLoc(interval.getContig(),interval.getStart()+maxShardSize,interval.getStop());
}
filePointers.add(new FilePointer(interval));
}
}
filePointerIterator = filePointers.iterator();
}