Temporary fix: have RodLocusView manage and close its RODs. Really the

relationship between these two classes needs to be rethought; see JIRA
GSA-207.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1904 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -26,11 +26,6 @@ import java.util.Collections;
  * A view into the reference-ordered data in the provider.
  */
 public class ManagingReferenceOrderedView implements ReferenceOrderedView {
-    /**
-     * The provider that's supplying our backing data.
-     */
-    //private final ShardDataProvider provider;
-
     /**
      * The data sources along with their current states.
      */
@@ -41,7 +36,6 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView {
      * @param provider
      */
     public ManagingReferenceOrderedView( ShardDataProvider provider ) {
-        //this.provider = provider;
         for( ReferenceOrderedDataSource dataSource: provider.getReferenceOrderedData() )
             states.add( new ReferenceOrderedDataState( dataSource, (SeekableRODIterator)dataSource.seek(provider.getShard()) ) );
 
@@ -72,11 +66,12 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView {
         // Clear out the existing data so that post-close() accesses to this data will fail-fast.
         states = null;
     }
+}
 
-    /**
+/**
  * Models the traversal state of a given ROD lane.
  */
-    private class ReferenceOrderedDataState {
+class ReferenceOrderedDataState {
     public final ReferenceOrderedDataSource dataSource;
     public final SeekableRODIterator iterator;
 
@@ -84,5 +79,4 @@ public class ManagingReferenceOrderedView implements ReferenceOrderedView {
         this.dataSource = dataSource;
         this.iterator = iterator;
     }
-    }
 }

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

@@ -39,6 +39,11 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
     // broken support for multi-locus rods
     //List<ReferenceOrderedDatum> multiLocusRODs = new LinkedList<ReferenceOrderedDatum>();
 
+    /**
+     * The data sources along with their current states.
+     */
+    private List<ReferenceOrderedDataState> states = new ArrayList<ReferenceOrderedDataState>();    
+
     /**
      * Enable debugging output -- todo remove me
      */
@@ -67,6 +72,8 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
             GenomeLoc shardLoc = provider.getShard().getGenomeLoc();
             it.seekForward(GenomeLocParser.createGenomeLoc(shardLoc.getContigIndex(), shardLoc.getStart()-1, shardLoc.getStart()-1));
 
+            states.add(new ReferenceOrderedDataState(dataSource,it));            
+
             // we need to special case the interval so we don't always think there's a rod at the first location
             if ( dataSource.getName().equals(INTERVAL_ROD_NAME) ) {
                 if ( interval != null )
@@ -202,6 +209,9 @@ public class RodLocusView extends LocusView implements ReferenceOrderedView {
      * Closes the current view.
      */
     public void close() {
+        for( ReferenceOrderedDataState state: states )
+            state.dataSource.close( state.iterator );        
+
         rodQueue = null;
         tracker = null;
     }