From 33be41ecf50012bf8234a015d22799cf60182b8e Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 17 Jul 2012 16:06:04 -0400
Subject: [PATCH] Cleaning up integration test

---
 .../sting/gatk/walkers/bqsr/BQSRIntegrationTest.java           | 3 +--
 .../sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java  | 2 +-
 2 files changed, 2 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 93dab8505..b9ea26e64 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
@@ -107,8 +107,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                 {new PRTest("", "d2d6ed8667cdba7e56f5db97d6262676")},
                 {new PRTest(" -qq -1", "b7053d3d67aba6d8892f0a60f0ded338")},
                 {new PRTest(" -qq 6", "bfbf0855185b2b70aa35237fb71e4487")},
-                {new PRTest(" -DIQ", "66aa65223f192ee39c1773aa187fd493")},
-                {new PRTest(" -EOQ", "")}
+                {new PRTest(" -DIQ", "66aa65223f192ee39c1773aa187fd493")}
         };
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java
index 299daebd9..1a99d51e6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java
@@ -185,7 +185,7 @@ public class BaseQualityScoreRecalibrator extends LocusWalker<Long, Long> implem
 
         Class c = null;
         for ( Class<? extends RecalibrationEngine> REclass : REclasses ) {
-            if ( REclass.isAssignableFrom(ProtectedPackageSource.class) ) {
+            if ( ProtectedPackageSource.class.isAssignableFrom(REclass) ) {
                 c = REclass;
                 break;
             }