Provide close methods to clean up resources used while creating AlignmentContexts from BAM file regions. Allows utilization of CoveredLocusView via the API

Signed-off-by: David Roazen <droazen@broadinstitute.org>

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java

@@ -246,6 +246,14 @@ public class BAMScheduler implements Iterator<FilePointer> {
      */
     private PeekableIterator<BAMScheduleEntry> bamScheduleIterator = null;
 
+    /**
+     * Clean up underlying BAMSchedule file handles.
+     */
+    public void close() {
+        if(bamScheduleIterator != null)
+            bamScheduleIterator.close();
+    }
+
     /**
      * Get the next overlapping tree of bins associated with the given BAM file.
      * @param currentLocus The actual locus for which to check overlap.

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java

@@ -62,6 +62,9 @@ public class IntervalSharder implements Iterator<FilePointer> {
         wrappedIterator = new PeekableIterator<FilePointer>(scheduler);
         this.parser = parser;
     }
+    public void close() {
+      wrappedIterator.close();
+    }
 
     public boolean hasNext() {
         return wrappedIterator.hasNext();

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -352,6 +352,14 @@ public class SAMDataSource {
         resourcePool.releaseReaders(readers);
     }
 
+    public void close() {
+        SAMReaders readers = resourcePool.getAvailableReaders();
+        for(SAMReaderID readerID: readerIDs) {
+            SAMFileReader reader = readers.getReader(readerID);
+            reader.close();
+        }
+    }
+
     /**
      * Returns Reads data structure containing information about the reads data sources placed in this pool as well as
      * information about how they are downsampled, sorted, and filtered

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java

@@ -43,4 +43,7 @@ public abstract class ShardBalancer implements Iterable<Shard> {
         this.filePointers = new PeekableIterator<FilePointer>(filePointers);
         this.parser = parser;
     }
+    public void close() {
+      this.filePointers.close();
+    }
 }