From e5e6d515c3384935bc89d10bef88d1faff199b56 Mon Sep 17 00:00:00 2001
From: alecw <alecw@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Nov 2009 15:12:49 +0000
Subject: [PATCH] Fix misunderstanding of GenomeLoc interval

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2138 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java
index 33b7e4d8b..59e1740af 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodPicardDbSNP.java
@@ -252,9 +252,9 @@ public class rodPicardDbSNP implements VariationRod {
 
     private static class MyGenomeLoc extends GenomeLoc {
         private MyGenomeLoc(final KnownVariant knownVariant) {
-            // GenomeLoc is one-based half-open interval.
+            // GenomeLoc is one-based closed interval.
             super(knownVariant.getReferenceSequence(), knownVariant.getSequenceIndex(), knownVariant.getStartPos(),
-                    knownVariant.getEndPos() + 1);
+                    knownVariant.getEndPos());
         }
     }