From 1cda87a4ad1d9d3a17eec9d8dea2bf6b5d0aede1 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Fri, 20 Apr 2012 14:51:21 -0400
Subject: [PATCH] Set ROD priority list to input

---
 .../sting/gatk/walkers/variantutils/SelectVariants.java        | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index b6a8123a9..106227f99 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -673,7 +673,8 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
         //defaults from CombineVariants
         VariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = VariantContextUtils.MultipleAllelesMergeType.BY_TYPE;
-        List<String> priority = new ArrayList<String>(VCFUtils.getVCFHeadersFromRods(getToolkit()).keySet());
+        List<String> priority = new ArrayList<String>();
+        priority.add("input");
         VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED;
         VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE;
         boolean printComplexMerges = false;