From ca737479cf240fa7221d25378cfa5961aaf97966 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Thu, 12 Apr 2012 16:17:42 -0400
Subject: [PATCH] Query for stop locations because we don't have that
 information in the reference

---
 .../sting/gatk/walkers/variantutils/SelectVariants.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 106227f99..1d4f8745e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -556,7 +556,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     private Collection<VariantContext> getMongoVariants(ReferenceContext ref, GenomeLoc location) {
         String contig = location.getContig();
         long start = location.getStart();
-        long stop = location.getStop();
 
         ArrayList<VariantContext> vcs = new ArrayList<VariantContext>();
 
@@ -642,6 +641,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             String source = (String)result.get("source");
             String id = (String)result.get("id");
             Double error = (Double)result.get("error");
+            Long stop = (Long)result.get("stop");
 
             VariantContextBuilder builder = new VariantContextBuilder(source, contig, start, stop, sourceRodAllelePair.getSecond());