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Fix for recent change modelling unmapped shards: don't invoke optimization to combine mapped and unmapped shards.

This commit is contained in:
Matt Hanna 2011-09-23 14:52:31 -04:00
parent f1f7335e7b
commit cc23b0b8a9
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
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@ -59,7 +59,7 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
*/
public FilePointer next() {
FilePointer current = wrappedIterator.next();
while(wrappedIterator.hasNext() && current.minus(wrappedIterator.peek()) == 0)
while(wrappedIterator.hasNext() && current.isRegionUnmapped == wrappedIterator.peek().isRegionUnmapped && current.minus(wrappedIterator.peek()) == 0)
current = current.combine(parser,wrappedIterator.next());
return current;
}