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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
This commit is contained in:
hanna 2010-02-01 20:27:06 +00:00
parent d9671dffba
commit d8e75cf631
1 changed files with 6 additions and 1 deletions
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7
java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
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@ -84,7 +84,7 @@ public class ShardDataProvider {
* Gets an iterator over all the reads bound by this shard. * Gets an iterator over all the reads bound by this shard.
* @return An iterator over all reads in this shard. * @return An iterator over all reads in this shard.
*/ */
StingSAMIterator getReadIterator() { public StingSAMIterator getReadIterator() {
return reads; return reads;
} }
@ -166,6 +166,11 @@ public class ShardDataProvider {
public void close() { public void close() {
for( View view: registeredViews ) for( View view: registeredViews )
view.close(); 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(); reads.close();
} }
} }