From 6a23edd9111b745c0abf9d8d385190a493c22db4 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 28 Jun 2010 21:51:48 +0000
Subject: [PATCH] Fix performance tests

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3662 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/indels/IndelRealignerPerformanceTest.java      | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
index 31bc87931..215e0e784 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
@@ -18,6 +18,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
                         " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
                         " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" +
                         " -L chr1:1-5,650,000" +
+                        " --realignReadsWithBadMates" +
                         " -targetIntervals " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.realigner.intervals",
                  0,
                 new ArrayList<String>(0));
@@ -32,6 +33,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest {
                         " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" +
                         " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" +
                         " -L chr1:1-150,000,000" +
+                        " --realignReadsWithBadMates" +
                         " -targetIntervals " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.realigner.intervals",
                  0,
                 new ArrayList<String>(0));