From a7fe847faf99fc83414713094e7fc691ab54050d Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Fri, 20 Apr 2012 14:18:19 -0400
Subject: [PATCH] Set the priority list and don't bother combining if not
 needed

---
 .../sting/gatk/walkers/variantutils/SelectVariants.java    | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

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 7590a8597..b6a8123a9 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
@@ -665,12 +665,15 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     }
 
     // Copied from CombineVariants
-    private Collection<VariantContext> combineVariants(ArrayList<VariantContext> vcs) {
+    private Collection<VariantContext> combineVariants(Collection<VariantContext> vcs) {
+        if (vcs.size() < 2)
+            return vcs;
+
         List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
 
         //defaults from CombineVariants
         VariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = VariantContextUtils.MultipleAllelesMergeType.BY_TYPE;
-        List<String> priority = null;
+        List<String> priority = new ArrayList<String>(VCFUtils.getVCFHeadersFromRods(getToolkit()).keySet());
         VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED;
         VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE;
         boolean printComplexMerges = false;