From 70980b659a038a66258ab3d3f51722891d5dc6d9 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 7 Dec 2010 15:39:43 +0000
Subject: [PATCH] CombineVariants no longer requires rod_priority_string

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4800 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantutils/CombineVariants.java     | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 048d820c2..efff0c750 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.SampleUtils;
+import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -81,9 +82,14 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
     private List<String> priority = null;
 
     public void initialize() {
-        validateAnnotateUnionArguments();
-
         Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), null);
+
+        if ( PRIORITY_STRING == null ) {
+            PRIORITY_STRING = Utils.join(",", vcfRods.keySet());
+            logger.info("Priority string not provided, using arbitrary genotyping order: " + PRIORITY_STRING);
+        }
+
+        validateAnnotateUnionArguments();
         Set<String> samples = SampleUtils.getSampleList(vcfRods, genotypeMergeOption);
 
         if ( SET_KEY.toLowerCase().equals("null") )