Interval-based traversals were bleeding file handles. Fixed.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@541 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java

@@ -95,6 +95,9 @@ public class TraverseByLoci extends TraversalEngine {
 
         //printOnTraversalDone("loci", sum);
         walker.onTraversalDone(sum);
+
+        samReader.close();
+
         return sum;
     }