From 1443ee8c7f3afd2c7c0a12c633ca2c9e37838dcf Mon Sep 17 00:00:00 2001
From: Mark Fleharty <fleharty@broadinstitute.org>
Date: Fri, 20 Nov 2015 11:23:02 -0500
Subject: [PATCH] Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql
 rather than -q1

---
 .../gatk/tools/walkers/bqsr/BQSRIntegrationTest.java            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
index a0382df91..b06de852d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java
@@ -292,7 +292,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                         " -R " + hg18Reference +
                         " -I " + HiSeqBam +
                         " -L " + HiSeqInterval +
-                        " -SQQ 4 -q1 4 " +
+                        " -SQQ 4 -ql 4 " +
                         " -BQSR " + privateTestDir + "HiSeq.1mb.1RG.lowMaxCycle.table" +
                         " -o /dev/null",
                 0,