From eafb4633ba3cb4f05caddda62dc7a72ba37f52cb Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 17 Apr 2009 23:14:41 +0000
Subject: [PATCH] Temporary workaround for samtools index bug: there seems to
 be an off-by-one error.  Will file bug report.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@470 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/dataSources/simpleDataSources/SAMDataSource.java     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
index 68bfdabf5..1a0643780 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
@@ -118,9 +118,9 @@ public class SAMDataSource implements SimpleDataSource {
 
         // we do different things for locus and read modes
         if (locusMode) {
-            iter.queryOverlapping(location.getContig(), (int) location.getStart(), (int) location.getStop());
+            iter.queryOverlapping(location.getContig(), (int) location.getStart(), (int) location.getStop()+1);
         } else {
-            iter.queryContained(location.getContig(), (int) location.getStart(), (int) location.getStop());
+            iter.queryContained(location.getContig(), (int) location.getStart(), (int) location.getStop()+1);
         }
 
         // return the iterator