From d7f98e5c2a174578ff4b967f9500631201f6d5ca Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 4 Aug 2011 18:48:34 -0400
Subject: [PATCH] Fixed merge conflict deleting a {

---
 .../sting/gatk/walkers/variantutils/VariantsToVCF.java | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index e3511ab11..07c5e71a6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -112,11 +112,13 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
                     vc = VariantContext.modifyGenotypes(vc, genotypes);
                 }
 
-            // todo - fix me. This may not be the cleanest way to handle features what need correct indel padding
-            if (fixReferenceBase) {
-                vc = new VariantContext("Variant",vc.getChr(),vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.getFilters(),vc.getAttributes(), ref.getBase());
+                // todo - fix me. This may not be the cleanest way to handle features what need correct indel padding
+                if (fixReferenceBase) {
+                    vc = new VariantContext("Variant",vc.getChr(),vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.getFilters(),vc.getAttributes(), ref.getBase());
+                }
+
+                writeRecord(vc, tracker, ref.getBase());
             }
-            writeRecord(vc, tracker, ref.getBase());
         }
 
         return 1;