From 4183e8805a3ada02011786160f830e8424cf57d0 Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 9 Sep 2010 20:34:51 +0000
Subject: [PATCH] Fixed reference (via busted symlink) /broad/1KG

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4245 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/alignment/AlignerIntegrationTest.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java b/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java
index 3e6f9bf67..d258d0481 100644
--- a/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java
@@ -16,7 +16,7 @@ public class AlignerIntegrationTest extends WalkerTest {
     public void testBasicAlignment() {
         String md5 = "c6d95d8ae707e78fefdaa7375f130995";
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R /humgen/gsa-scr1/GATK_Data/bwa/human_b36_both.fasta" +
+                        "-R " + b36KGReference +
                         " -T Align" +
                         " -I " + validationDataLocation + "NA12878_Pilot1_20.trimmed.unmapped.bam" +
                         " -ob %s",