From d170187896bc58200a2e827373046b03c4c260cd Mon Sep 17 00:00:00 2001 From: Matt Hanna Date: Wed, 17 Aug 2011 16:16:05 -0400 Subject: [PATCH] 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. --- .../gatk/datasources/reads/LowMemoryIntervalSharder.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java index ba6321121..198f7d7d3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java @@ -59,8 +59,8 @@ public class LowMemoryIntervalSharder implements Iterator { */ public FilePointer next() { FilePointer current = wrappedIterator.next(); - while(wrappedIterator.hasNext() && current.minus(wrappedIterator.peek()) == 0) - current = current.combine(parser,wrappedIterator.next()); + //while(wrappedIterator.hasNext() && current.minus(wrappedIterator.peek()) == 0) + // current = current.combine(parser,wrappedIterator.next()); return current; }