From 1daa0113871e72721367433c298ef9ddc59edac4 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 26 Apr 2009 18:35:54 +0000
Subject: [PATCH] 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
---
 .../broadinstitute/sting/gatk/traversals/TraverseByLoci.java   | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
index 7cc847cd1..9b0d630ba 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java
+++ b/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;
     }