From b7e4a015c019cac359a5f5d4eee70a58f4f7e901 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 17 Dec 2010 21:53:10 +0000
Subject: [PATCH] static thread cache reset in UnitTest

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4870 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../fasta/CachingIndexedFastaSequenceFile.java   | 16 ++++++++++++----
 .../CachingIndexedFastaSequenceFileUnitTest.java |  7 +++++++
 2 files changed, 19 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
index ebafc4cb6..9b2550bfd 100644
--- a/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
@@ -67,12 +67,20 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
         ReferenceSequence seq = null;
     }
 
-    private static ThreadLocal<Cache> cache = new ThreadLocal<Cache> () {
-        @Override protected Cache initialValue() {
-            return new Cache();
-        }
+    private static ThreadLocal<Cache> cache;
+
+    static {
+        resetThreadLocalCache();
     };
 
+    protected static void resetThreadLocalCache() {
+        cache = new ThreadLocal<Cache> () {
+            @Override protected Cache initialValue() {
+                return new Cache();
+            }
+        };
+    }
+
     /**
      * Same as general constructor but allows one to override the default cacheSize
      * @param file
diff --git a/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
index aa720e521..4d284d2e2 100644
--- a/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
@@ -8,6 +8,8 @@ package org.broadinstitute.sting.utils.fasta;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 import org.testng.annotations.DataProvider;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.BeforeMethod;
 import org.broadinstitute.sting.BaseTest;
 
 import java.io.File;
@@ -30,6 +32,11 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest {
     private static final List<Integer> QUERY_SIZES = Arrays.asList(1, 10, 100, 1000);
     private static final List<Integer> CACHE_SIZES = Arrays.asList(-1, 10, 1000);
 
+    @BeforeTest
+    public void clearCache() {
+        CachingIndexedFastaSequenceFile.resetThreadLocalCache();
+    }
+
     @DataProvider(name = "fastas")
     public Object[][] createData1() {
         List<Object[]> params = new ArrayList<Object[]>();