From 7748b3816f30cb5a4f6729f1cf6451634bfd241e Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Mon, 31 Dec 2012 17:22:57 -0500
Subject: [PATCH] Delete the test BAI file as well as the BAM

---
 .../sting/gatk/traversals/TraverseActiveRegionsTest.java       | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
index f276d21e5..f37c2ce63 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
@@ -104,6 +104,7 @@ public class TraverseActiveRegionsTest extends BaseTest {
     private List<GenomeLoc> intervals;
 
     private static final String testBAM = "TraverseActiveRegionsTest.bam";
+    private static final String testBAI = "TraverseActiveRegionsTest.bai";
 
     @BeforeClass
     private void init() throws FileNotFoundException {
@@ -149,6 +150,8 @@ public class TraverseActiveRegionsTest extends BaseTest {
     private void createBAM(List<GATKSAMRecord> reads) {
         File outFile = new File(testBAM);
         outFile.deleteOnExit();
+        File indexFile = new File(testBAI);
+        indexFile.deleteOnExit();
 
         SAMFileWriter out = new SAMFileWriterFactory().makeBAMWriter(reads.get(0).getHeader(), true, outFile);
         for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) {