From 2f5d10d16bd9e53b293c1a913e9f7a3cd601784f Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Thu, 21 Jul 2011 13:21:48 -0400
Subject: [PATCH] Fix bug wherein aligner could be closed prior to its being
 used to lowercase sequences.

---
 .../sting/gatk/walkers/validation/ValidationAmplicons.java    | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
index 7e39d2658..cb03d4c61 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
@@ -228,14 +228,12 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
     }
 
     public void onTraversalDone(Integer fin ) {
-        if(aligner != null)
-            aligner.close();
-
         validateSequence();
         if ( doNotUseBWA ) {
             lowerRepeats();
         } else {
             lowerNonUniqueSegments();
+            aligner.close();
         }
         print();
     }