From 2d28972c882e140d42b08bde465627ede1b7a9f3 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Sat, 30 Aug 2014 03:04:54 +0800
Subject: [PATCH] The 'after' files are @Input files and commited in git, so
 don't delete them after tests.

---
 .../tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java     | 1 -
 1 file changed, 1 deletion(-)

diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
index 485e3ddda..4dd20fc47 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
@@ -147,7 +147,6 @@ public class AnalyzeCovariatesIntegrationTest extends WalkerTest {
             throws IOException  {
 
         final File afterFile = new File(TEST_DATA_DIR,afterFileName);
-        afterFile.deleteOnExit();
         final WalkerTestSpec spec = new WalkerTestSpec(
                 buildCommandLine(null,"%s",true,true,afterFile),
                 1,UserException.IncompatibleRecalibrationTableParameters.class);