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Disable optimization that increases marginal speed of the GATK slightly but 

can produce data loss in a narrow corner case where the BGZF block(s) locations
and offsets in the last index bucket of contig n overlap exactly with the BGZF
block locations and offset in the last index bucket of contig n+1.

A proper fix that keeps the optimization has already been introduced into
unstable, but disabling the optimization is a low risk way to make sure that
users of stable experience no data loss.
This commit is contained in:
Matt Hanna 2011-08-17 16:16:05 -04:00
parent 1afc49a297
commit d170187896
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
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@ -59,8 +59,8 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
*/ */
public FilePointer next() { public FilePointer next() {
FilePointer current = wrappedIterator.next(); FilePointer current = wrappedIterator.next();
while(wrappedIterator.hasNext() && current.minus(wrappedIterator.peek()) == 0) //while(wrappedIterator.hasNext() && current.minus(wrappedIterator.peek()) == 0)
current = current.combine(parser,wrappedIterator.next()); // current = current.combine(parser,wrappedIterator.next());
return current; return current;
} }