From 06e3c34e7ff5eb5736e6f7a048feeab1f1225ab8 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 24 Feb 2011 20:13:35 +0000
Subject: [PATCH] Updating performance test to be in sync with previous commit

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5308 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/indels/IndelRealignerPerformanceTest.java      | 2 --
 1 file changed, 2 deletions(-)

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 948fa3e4a..f32a2b156 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
@@ -18,7 +18,6 @@ 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));
@@ -33,7 +32,6 @@ 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));