From dd30ad751a8be50f5a4b392fcf96c2f3593440c1 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 1 Mar 2011 17:11:22 +0000
Subject: [PATCH] Fix bug in low memory sharder's interval accumulator.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5345 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/reads/LowMemoryIntervalSharder.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
index bde5cb9f7..40c2cb1af 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/reads/LowMemoryIntervalSharder.java
@@ -119,7 +119,7 @@ public class LowMemoryIntervalSharder implements Iterator<FilePointer> {
             if(!nextFilePointer.locations.isEmpty()) {
                 while(locusIterator.hasNext() && locusIterator.peek().overlapsP(coveredRegion)) {
                     currentLocus = locusIterator.next();
-                    nextFilePointer.addLocation(locusIterator.next());
+                    nextFilePointer.addLocation(currentLocus.intersect(coveredRegion));
                 }
 
                 // Chop off the uncovered portion of the locus.  Since we know that the covered region overlaps the current locus,