From d647ea4fdc4274507d0456c955f2dfbf66ae70c1 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Fri, 1 Jul 2011 16:04:30 -0400
Subject: [PATCH] Long-delayed change to CachingIndexedFastaSequenceFile. Made
 the cache non-static to avoid problems when multiple references are used
 within the same thread (eg., during integration tests). This should kill the
 intermittent IndelRealignerIntegrationTest failures.

---
 .../utils/fasta/CachingIndexedFastaSequenceFile.java      | 8 ++++----
 .../fasta/CachingIndexedFastaSequenceFileUnitTest.java    | 5 -----
 2 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
index bda52dd4e..0c5085cc7 100644
--- a/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
+++ b/public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
@@ -68,13 +68,13 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
         ReferenceSequence seq = null;
     }
 
-    private static ThreadLocal<Cache> cache;
+    private ThreadLocal<Cache> cache;
 
-    static {
+    {
         resetThreadLocalCache();
-    };
+    }
 
-    protected static void resetThreadLocalCache() {
+    protected void resetThreadLocalCache() {
         cache = new ThreadLocal<Cache> () {
             @Override protected Cache initialValue() {
                 return new Cache();
diff --git a/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
index a60f1b0fe..74cd8d8fe 100644
--- a/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
@@ -34,11 +34,6 @@ 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);
 
-    @BeforeMethod
-    public void clearCache() {
-        CachingIndexedFastaSequenceFile.resetThreadLocalCache();
-    }
-
     @DataProvider(name = "fastas")
     public Object[][] createData1() {
         List<Object[]> params = new ArrayList<Object[]>();