From b59d62927e81538ac3a2f43fb6d687d889f7295b Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Sep 2010 12:51:53 +0000
Subject: [PATCH] Fix busted performance test (-outputBam has been deprecated
 in the BQ recalibrator in favor of -o)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4201 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../recalibration/RecalibrationWalkersPerformanceTest.java    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
index 3a77ce7e6..7b293e5ff 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
@@ -55,7 +55,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -L chr1:1-50,000,000" +
                         " -OQ" +
                         " -recalFile " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.recal.csv" +
-                        " -outputBam /dev/null",
+                        " -o /dev/null",
                 0,
                 new ArrayList<String>(0));
         executeTest("testTableRecalibratorWholeGenome", spec);
@@ -70,7 +70,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest {
                         " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" +
                         " -OQ" +
                         " -recalFile " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.recal.csv" +
-                        " -outputBam /dev/null",
+                        " -o /dev/null",
                 0,
                 new ArrayList<String>(0));
         executeTest("testTableRecalibratorWholeExome", spec);