From df965d4a5a9b9466240f81dda517a6d5c04cf8f4 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sat, 21 Jul 2012 10:52:59 -0400
Subject: [PATCH] Fixing BQSR integration test

---
 .../sting/gatk/walkers/bqsr/BQSRIntegrationTest.java        | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
index dd96dfeb9..635a74399 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
@@ -59,7 +59,7 @@ public class BQSRIntegrationTest extends WalkerTest {
     @Test(dataProvider = "BQSRTest")
     public void testBQSR(BQSRTest params) {
         WalkerTestSpec spec = new WalkerTestSpec(
-                "-T BaseQualityScoreRecalibrator" +
+                " -T BQSR" +
                         " -R " + params.reference +
                         " -I " + params.bam +
                         " -L " + params.interval +
@@ -74,8 +74,8 @@ public class BQSRIntegrationTest extends WalkerTest {
     @Test
     public void testBQSRFailWithoutDBSNP() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R " + b36KGReference +
-                        " -T BaseQualityScoreRecalibrator" +
+                " -T BQSR" +
+                        " -R " + b36KGReference +
                         " -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" +
                         " -L 1:10,000,000-10,200,000" +
                         " --no_plots" +