From caf2c21f613fa189fccec06c764aec36009190f2 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 24 Nov 2010 04:33:08 +0000
Subject: [PATCH] Must close the writer to flush the cache

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4726 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/LeftAlignVariants.java       | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index 41f522eea..485af6261 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -90,6 +90,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
     }
 
     public void onTraversalDone(Integer result) {
+        writer.close();
         System.out.println(result + " variants were aligned");
     }