From a4fa02f11c3ae6e9465cfff6b8d340973bebc98f Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 18 Jun 2009 19:59:26 +0000
Subject: [PATCH] Moved output outside of for loop so I don't have 10 different
 versions of the same variant (though, now that I think of it, that's not
 necessarily a terrible thing for debugging...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1045 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variants/VariantFiltrationWalker.java         | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
index 865593e47..9f35d26c6 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VariantFiltrationWalker.java
@@ -49,8 +49,9 @@ public class VariantFiltrationWalker extends LocusWalker<Integer, Integer> {
             else { throw new StingException(String.format("Cannot understand feature '%s'", featureName)); }
 
             variant.adjustLikelihoods(ivf.compute(ref, context));
-            vwriter.println(variant);
         }
+        
+        vwriter.println(variant);
 
         return 1;
     }