From d8e75cf63168c930d67edb85186e5cdae08c39ca Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 1 Feb 2010 20:27:06 +0000
Subject: [PATCH] Fix for Kiran's memory issue running UG...turned out to be a
 particularly bad interaction between @By(Reference) traversals and
 TreeReduce.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2757 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/datasources/providers/ShardDataProvider.java      | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
index b5acf6e78..4c0ce57e5 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
@@ -84,7 +84,7 @@ public class ShardDataProvider {
      * Gets an iterator over all the reads bound by this shard.
      * @return An iterator over all reads in this shard.
      */
-    StingSAMIterator getReadIterator() {
+    public StingSAMIterator getReadIterator() {
         return reads;
     }
 
@@ -166,6 +166,11 @@ public class ShardDataProvider {
     public void close() {
         for( View view: registeredViews )
             view.close();
+
+        // Explicitly purge registered views to ensure that we don't end up with circular references
+        // to views, which can in turn hold state.
+        registeredViews.clear();
+
         reads.close();
     }
 }