From 4cafb95be874a00830b857659f4d6efa88d88566 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 22 Apr 2009 15:48:20 +0000
Subject: [PATCH] TraverseByLoci / TraverseByLociByReference suffered from the
 same sam-triggered off-by-one (?) bug as TraverseByReference; it was just
 less obvious here because these versions don't shard.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@491 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/traversals/TraverseByLoci.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
index 416521a21..599d3725d 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
@@ -79,7 +79,7 @@ public class TraverseByLoci extends TraversalEngine {
 
                 CloseableIterator<SAMRecord> readIter = samReader.queryOverlapping( interval.getContig(),
                         (int)interval.getStart(),
-                        (int)interval.getStop() );
+                        (int)interval.getStop()+1 );
 
                 Iterator<SAMRecord> wrappedIter = WrapReadsIterator( readIter, false );
                 sum = carryWalkerOverInterval(walker, wrappedIter, sum, interval);