The TraversalEngine's habit of hanging onto old ROD states seems to have a bad

interaction with Tribble.  In Tribble, keeping these references in memory until
the shard is flushed means keeping one 512K character buffer per object in
memory.  Fixed by purging the reference to the object at the end of the 
shard traversal.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4599 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java

@@ -62,6 +62,7 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView {
     public void close() {
         for( ReferenceOrderedDataState state: states )
             state.dataSource.close( state.iterator );
+        states.clear();
 
         // Clear out the existing data so that post-close() accesses to this data will fail-fast.
         states = null;

java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java

@@ -208,6 +208,7 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
     public void close() {
         for( ReferenceOrderedDataState state: states )
             state.dataSource.close( state.iterator );
+        states.clear();
 
         rodQueue = null;
         tracker = null;