From 78a4d8ec3ddefe41206cf842456a3efa914ec826 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 14 Jul 2010 16:34:15 +0000
Subject: [PATCH] Removing more references to VCFRecord

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3790 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../variantrecalibration/ApplyVariantCuts.java   | 16 ++--------------
 .../sting/utils/genotype/vcf/VCFUtils.java       | 13 -------------
 2 files changed, 2 insertions(+), 27 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
index 5d1d16bc0..52035108d 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
@@ -29,15 +29,12 @@ import org.broad.tribble.vcf.*;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
-import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.genotype.vcf.VCFReader;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter;
 import org.broadinstitute.sting.utils.text.XReadLines;
@@ -106,17 +103,8 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
         hInfo.add(new VCFHeaderLine("source", "VariantOptimizer"));
         vcfWriter = new VCFWriter( new File(OUTPUT_FILENAME) );
         final TreeSet<String> samples = new TreeSet<String>();
-        final List<ReferenceOrderedDataSource> dataSources = this.getToolkit().getRodDataSources();
-        for( final ReferenceOrderedDataSource source : dataSources ) {
-            final RMDTrack rod = source.getReferenceOrderedData();
-            if( rod.getRecordType().equals(VCFRecord.class) ) {
-                final VCFReader reader = new VCFReader(rod.getFile());
-                final Set<String> vcfSamples = reader.getHeader().getGenotypeSamples();
-                samples.addAll(vcfSamples);
-                reader.close();
-            }
-        }
-
+        samples.addAll(SampleUtils.getSampleListWithVCFHeader(getToolkit(), null));
+        
         for( int iii = 1; iii < filterName.size(); iii++ ) {
             hInfo.add(new VCFFilterHeaderLine(filterName.get(iii), String.format("FDR tranche level at qual " + qCuts.get(iii))));
         }
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 29cdc7cda..d68e9a274 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
@@ -45,19 +45,6 @@ public class VCFUtils {
      */
     private VCFUtils() { }
 
-    public static Set<RMDTrack> getRodVCFs(GenomeAnalysisEngine toolkit) {
-        Set<RMDTrack> vcfs = new HashSet<RMDTrack>();
-
-        for ( ReferenceOrderedDataSource source : toolkit.getRodDataSources() ) {
-            RMDTrack rod = source.getReferenceOrderedData();
-            if ( rod.getRecordType().equals(VCFRecord.class) ) {
-                vcfs.add(rod);
-            }
-        }
-
-        return vcfs;
-    }
-
     /**
      * Gets the header fields from all VCF rods input by the user
      *