From bf384f48e1014410120c421c3d9e265905fb3d04 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 14 Jul 2010 19:13:17 +0000
Subject: [PATCH] Reverting previous change because it won't always work.  More
 investigation needed.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3793 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java  | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
index 3751d871c..d68e9a274 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
@@ -61,7 +61,7 @@ public class VCFUtils {
         List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
         for ( ReferenceOrderedDataSource source : dataSources ) {
             RMDTrack rod = source.getReferenceOrderedData();
-            if ( rod.getHeader() instanceof VCFHeader ) {
+            if ( rod.getRecordType().equals(VCFRecord.class) ) {
                 fields.addAll(rod.getHeader(VCFHeader.class).getMetaData());                
             }
         }
@@ -126,6 +126,7 @@ public class VCFUtils {
 
     public static Set<VCFHeaderLine> smartMergeHeaders(Collection<VCFHeader> headers, Logger logger) throws IllegalStateException {
         HashMap<String, VCFHeaderLine> map = new HashMap<String, VCFHeaderLine>(); // from KEY.NAME -> line
+        HashSet<VCFHeaderLine> lines = new HashSet<VCFHeaderLine>();
 
         // todo -- needs to remove all version headers from sources and add its own VCF version line
         for ( VCFHeader source : headers ) {