Refactored and generalized the VCF header info code.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2346 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.genotype.*;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.List;
 import java.util.Map;
@@ -61,5 +62,5 @@ public class AlleleBalance extends StandardVariantAnnotation {
 
     public String getKeyName() { return "AB"; }
 
-    public String getDescription() { return "AB,1,Float,\"Allele Balance for hets (ref/(ref+alt))\""; }
+    public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine("AB", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Allele Balance for hets (ref/(ref+alt))"); }
 }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
@@ -19,5 +20,5 @@ public class DepthOfCoverage extends StandardVariantAnnotation {
 
     public String getKeyName() { return VCFRecord.DEPTH_KEY; }
 
-    public String getDescription() { return getKeyName() + ",1,Integer,\"Total Depth (including MQ0 reads)\""; }
+    public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(getKeyName(), 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Total Depth (including MQ0 reads)"); }
 }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.genotype.Variation;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
@@ -21,7 +22,7 @@ public class HomopolymerRun extends StandardVariantAnnotation {
 
     public String getKeyName() { return "HRun"; }
 
-    public String getDescription() { return "HRun,1,Integer,\"Largest Contiguous Homopolymer Run of Variant Allele In Either Direction\""; }
+    public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine("HRun", 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Largest Contiguous Homopolymer Run of Variant Allele In Either Direction"); }
 
     public boolean useZeroQualityReads() { return false; }
 

java/src/org/broadinstitute/sting/gatk/walkers/annotator/MismatchRate.java

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.genotype.Variation;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.*;
 
 import java.util.Map;
@@ -30,5 +31,5 @@ public class MismatchRate implements VariantAnnotation {
 
     public String getKeyName() { return "MR"; }
 
-    public String getDescription() { return "MR,1,Float,\"Mismatch Rate of Reads Spanning This Position\""; }
+    public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine("MR", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Mismatch Rate of Reads Spanning This Position"); }
 }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java

@@ -7,6 +7,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 import java.util.ArrayList;
@@ -31,5 +32,5 @@ public class RMSMappingQuality extends StandardVariantAnnotation {
 
     public String getKeyName() { return VCFRecord.RMS_MAPPING_QUALITY_KEY; }
 
-    public String getDescription() { return getKeyName() + ",1,Float,\"RMS Mapping Quality\""; }
+    public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(getKeyName(), 1, VCFInfoHeaderLine.INFO_TYPE.Float, "RMS Mapping Quality"); }
 }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java

@@ -6,6 +6,7 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.*;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.List;
 import java.util.ArrayList;
@@ -67,7 +68,7 @@ public class RankSumTest implements VariantAnnotation {
 
     public String getKeyName() { return "RankSum"; }
 
-    public String getDescription() { return "RankSum,1,Float,\"Phred-scaled p-value From Wilcoxon Rank Sum Test of Het Vs. Ref Base Qualities\""; }
+    public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine("RankSum", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Phred-scaled p-value From Wilcoxon Rank Sum Test of Het Vs. Ref Base Qualities"); }
 
     private void fillQualsFromPileup(char ref, char alt, ReadBackedPileup pileup, List<Integer> refQuals, List<Integer> altQuals) {
         for ( PileupElement p : pileup ) {

java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.Variation;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 
@@ -26,7 +27,7 @@ public class SecondBaseSkew implements VariantAnnotation {
 
     public String getKeyName() { return KEY_NAME; }
 
-    public String getDescription() { return KEY_NAME + ",1,Float,\"Chi-square Secondary Base Skew\""; }
+    public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine(KEY_NAME, 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Chi-square Secondary Base Skew"); }
 
     public String annotate(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, Variation variation) {
         if ( !variation.isBiallelic() || !variation.isSNP() )

java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.Variation;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
@@ -23,5 +24,5 @@ public class SpanningDeletions extends StandardVariantAnnotation {
 
     public String getKeyName() { return "Dels"; }
 
-    public String getDescription() { return "Dels,1,Float,\"Fraction of Reads Containing Spanning Deletions\""; }
+    public VCFInfoHeaderLine getDescription() { return new VCFInfoHeaderLine("Dels", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Fraction of Reads Containing Spanning Deletions"); }
 }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
 import org.broadinstitute.sting.utils.genotype.Variation;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 
@@ -16,6 +17,6 @@ public interface VariantAnnotation {
     public String getKeyName();
 
     // return the description used for the VCF INFO meta field
-    public String getDescription();
+    public VCFInfoHeaderLine getDescription();
 
 }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -116,10 +116,10 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         }
 
         // setup the header fields
-        Set<String> hInfo = new HashSet<String>();
+        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
-        hInfo.add("source=VariantAnnotator");
+        hInfo.add(new VCFHeaderLine("source", "VariantAnnotator"));
-        hInfo.add("annotatorReference=" + getToolkit().getArguments().referenceFile.getName());
+        hInfo.add(new VCFHeaderLine("annotatorReference", getToolkit().getArguments().referenceFile.getName()));
         hInfo.addAll(getVCFAnnotationDescriptions(requestedAnnotations));
 
         vcfHeader = new VCFHeader(hInfo, samples);
@@ -175,35 +175,35 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
     }
 
     // option #1: don't specify annotations to be used: standard annotations are used by default
-    public static Set<String> getVCFAnnotationDescriptions() {
+    public static Set<VCFHeaderLine> getVCFAnnotationDescriptions() {
         if ( standardAnnotations == null )
             determineAllAnnotations();
 
-        TreeSet<String> descriptions = new TreeSet<String>();
+        TreeSet<VCFHeaderLine> descriptions = new TreeSet<VCFHeaderLine>();
         for ( VariantAnnotation annotation : standardAnnotations.values() )
-            descriptions.add("INFO=" + annotation.getDescription());
+            descriptions.add(annotation.getDescription());
 
         return descriptions;
     }
 
     // option #2: specify that all possible annotations be used
-    public static Set<String> getAllVCFAnnotationDescriptions() {
+    public static Set<VCFHeaderLine> getAllVCFAnnotationDescriptions() {
         if ( standardAnnotations == null )
             determineAllAnnotations();
 
-        TreeSet<String> descriptions = new TreeSet<String>();
+        TreeSet<VCFHeaderLine> descriptions = new TreeSet<VCFHeaderLine>();
         for ( VariantAnnotation annotation : allAnnotations.values() )
-            descriptions.add("INFO=" + annotation.getDescription());
+            descriptions.add(annotation.getDescription());
 
         return descriptions;
     }
 
     // option #3: specify the exact annotations to be used
-    public static Set<String> getVCFAnnotationDescriptions(Collection<VariantAnnotation> annotations) {
+    public static Set<VCFHeaderLine> getVCFAnnotationDescriptions(Collection<VariantAnnotation> annotations) {
 
-        TreeSet<String> descriptions = new TreeSet<String>();
+        TreeSet<VCFHeaderLine> descriptions = new TreeSet<VCFHeaderLine>();
         for ( VariantAnnotation annotation : annotations )
-            descriptions.add("INFO=" + annotation.getDescription());
+            descriptions.add(annotation.getDescription());
 
         return descriptions;
     }

java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java

@@ -103,21 +103,21 @@ public class CallsetConcordanceWalker extends RodWalker<Integer, Integer> {
         }
 
         // set up the header fields
-        Set<String> hInfo = new HashSet<String>();
+        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
-        hInfo.add("source=CallsetConcordance");
+        hInfo.add(new VCFHeaderLine("source", "CallsetConcordance"));
-        hInfo.add("note=\"This file represents a concordance test of various call sets - NOT the output from a multi-sample caller\"");
+        hInfo.add(new VCFHeaderLine("note", "\"This file represents a concordance test of various call sets - NOT the output from a multi-sample caller\""));
         hInfo.addAll(getVCFAnnotationDescriptions(requestedTypes));
         VCFHeader header = new VCFHeader(hInfo, samples);
 
         vcfWriter = new VCFWriter(header, OUTPUT);
     }
 
-    public static Set<String> getVCFAnnotationDescriptions(Collection<ConcordanceType> types) {
+    public static Set<VCFHeaderLine> getVCFAnnotationDescriptions(Collection<ConcordanceType> types) {
 
-        TreeSet<String> descriptions = new TreeSet<String>();
+        TreeSet<VCFHeaderLine> descriptions = new TreeSet<VCFHeaderLine>();
         for ( ConcordanceType type : types )
-            descriptions.add("INFO=" + type.getInfoDescription());
+            descriptions.add(type.getInfoDescription());
 
         return descriptions;
     }

java/src/org/broadinstitute/sting/gatk/walkers/concordance/ConcordanceType.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.concordance;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.Map;
 import java.util.Set;
@@ -11,5 +12,5 @@ public interface ConcordanceType {
     public void initialize(Map<String,String> args, Set<String> samples);
     public String computeConcordance(Map<String, Genotype> samplesToRecords, ReferenceContext ref);
     public String getInfoName();
-    public String getInfoDescription();
+    public VCFInfoHeaderLine getInfoDescription();
 }

java/src/org/broadinstitute/sting/gatk/walkers/concordance/IndelSubsets.java

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.*;
 
@@ -102,5 +103,5 @@ public class IndelSubsets implements ConcordanceType {
     }
 
     public String getInfoName() { return "IndelSubsets"; }
-    public String getInfoDescription() { return getInfoName() + ",1,String,\"Indel-related subsets\""; }    
+    public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "Indel-related subsets"); }    
 }

java/src/org/broadinstitute/sting/gatk/walkers/concordance/NWayVenn.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.concordance;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.*;
 import java.util.Map.Entry;
@@ -39,5 +40,5 @@ public class NWayVenn implements ConcordanceType {
     }
 
     public String getInfoName() { return "NwayVenn"; }    
-    public String getInfoDescription() { return getInfoName() + ",1,String,\"N-way Venn split\""; }
+    public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "N-way Venn split"); }
 }

java/src/org/broadinstitute/sting/gatk/walkers/concordance/SNPGenotypeConcordance.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.concordance;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import java.util.*;
 
@@ -111,5 +112,5 @@ public class SNPGenotypeConcordance implements ConcordanceType {
     }
 
     public String getInfoName() { return "SnpConcordance"; }    
-    public String getInfoDescription() { return getInfoName() + ",1,String,\"SNP concordance test\""; }    
+    public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "SNP concordance test"); }    
 }

java/src/org/broadinstitute/sting/gatk/walkers/concordance/SimpleVenn.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.concordance;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.genotype.Variation;
 import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
@@ -59,5 +60,5 @@ public class SimpleVenn implements ConcordanceType {
     }
 
     public String getInfoName() { return "Venn"; }
-    public String getInfoDescription() { return getInfoName() + ",1,String,\"2-way Venn split\""; }    
+    public VCFInfoHeaderLine getInfoDescription() { return new VCFInfoHeaderLine(getInfoName(), 1, VCFInfoHeaderLine.INFO_TYPE.String, "2-way Venn split"); }    
 }

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -47,18 +47,19 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
 
     private void initializeVcfWriter(RodVCF rod) {
         // setup the header fields
-        Set<String> hInfo = new HashSet<String>();
+        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
-        hInfo.add("source=" + "VariantFiltration");
+        hInfo.add(new VCFHeaderLine("source", "VariantFiltration"));
-        hInfo.add("reference=" + getToolkit().getArguments().referenceFile.getName());
+        hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
+
         if ( clusterWindow > 0 )
-            hInfo.add("FILTER=" + CLUSTERED_SNP_FILTER_NAME + ",\"SNPs found in clusters\"");
+            hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters"));
         if ( filterExpression != null )
-            hInfo.add("FILTER=" + FILTER_NAME + ",\"" + FILTER_STRING + "\"");
+            hInfo.add(new VCFFilterHeaderLine(FILTER_NAME, FILTER_STRING));
         List<ReferenceOrderedDataSource> dataSources = getToolkit().getRodDataSources();
         for ( ReferenceOrderedDataSource source : dataSources ) {
             if ( source.getReferenceOrderedData().getName().equals("mask") ) {
-                hInfo.add("FILTER=" + MASK_NAME + ",\"Overlaps a user-input mask\"");
+                hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
                 break;
             }
         }

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -37,6 +37,8 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.cmdLine.*;
 import org.broadinstitute.sting.utils.genotype.*;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
 
 import net.sf.samtools.SAMReadGroupRecord;
 
@@ -139,7 +141,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
             samples.clear();
 
         // get the optional header fields
-        Set<String> headerInfo = getHeaderInfo();
+        Set<VCFHeaderLine> headerInfo = getHeaderInfo();
 
         // create the output writer stream
         if ( VARIANTS_FILE != null )
@@ -154,16 +156,16 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
         callsMetrics = new CallMetrics();
     }
 
-    private Set<String> getHeaderInfo() {
+    private Set<VCFHeaderLine> getHeaderInfo() {
-        Set<String> headerInfo = new HashSet<String>();
+        Set<VCFHeaderLine> headerInfo = new HashSet<VCFHeaderLine>();
 
         // this is only applicable to VCF
         if ( UAC.VAR_FORMAT != GenotypeWriterFactory.GENOTYPE_FORMAT.VCF )
             return headerInfo;
 
         // first, the basic info
-        headerInfo.add("source=UnifiedGenotyper");
+        headerInfo.add(new VCFHeaderLine("source", "UnifiedGenotyper"));
-        headerInfo.add("reference=" + getToolkit().getArguments().referenceFile.getName());
+        headerInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
         // annotation (INFO) fields from VariantAnnotator
         if ( UAC.ALL_ANNOTATIONS )
@@ -172,10 +174,10 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
             headerInfo.addAll(VariantAnnotator.getVCFAnnotationDescriptions());
 
         // annotation (INFO) fields from UnifiedGenotyper
-        headerInfo.add("INFO=AF,1,Float,\"Allele Frequency\"");
+        headerInfo.add(new VCFInfoHeaderLine("AF", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Allele Frequency"));
-        headerInfo.add("INFO=NS,1,Integer,\"Number of Samples With Data\"");
+        headerInfo.add(new VCFInfoHeaderLine("NS", 1, VCFInfoHeaderLine.INFO_TYPE.Integer, "Number of Samples With Data"));
         if ( !UAC.NO_SLOD )
-            headerInfo.add("INFO=SB,1,Float,\"Strand Bias\"");
+            headerInfo.add(new VCFInfoHeaderLine("SB", 1, VCFInfoHeaderLine.INFO_TYPE.Float, "Strand Bias"));
 
         // FORMAT fields if not in POOLED mode
         if ( UAC.genotypeModel != GenotypeCalculationModel.Model.POOLED )
@@ -184,7 +186,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
         // all of the arguments from the argument collection
         Map<String,String> commandLineArgs = CommandLineUtils.getApproximateCommandLineArguments(Collections.<Object>singleton(UAC));
         for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() )
-            headerInfo.add(String.format("UG_%s=%s", commandLineArg.getKey(), commandLineArg.getValue()));            
+            headerInfo.add(new VCFHeaderLine(String.format("UG_%s", commandLineArg.getKey()), commandLineArg.getValue()));            
 
         return headerInfo;
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java

@@ -59,9 +59,9 @@ public class VariantsToVCF extends RefWalker<Integer, Integer> {
         //Calendar cal = Calendar.getInstance();
         //metaData.put("fileDate", String.format("%d%02d%02d", cal.get(Calendar.YEAR), cal.get(Calendar.MONTH), cal.get(Calendar.DAY_OF_MONTH)));
 
-        Set<String> metaData = new HashSet<String>();
+        Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
-        metaData.add("source=VariantsToVCF");
+        metaData.add(new VCFHeaderLine("source", "VariantsToVCF"));
-        metaData.add("reference=" + args.referenceFile.getAbsolutePath());
+        metaData.add(new VCFHeaderLine("reference", args.referenceFile.getAbsolutePath()));
 
         Set<String> additionalColumns = new HashSet<String>();
         additionalColumns.add("FORMAT");

java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java

@@ -33,9 +33,9 @@ public class VCFSubsetWalker extends RefWalker<ArrayList<VCFRecord>, VCFWriter>
 
     public void initializeWriter() {
 
-        Set<String> metaData = new HashSet<String>();
+        Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
-        metaData.add("source=VariantsToVCF");
+        metaData.add(new VCFHeaderLine("source", "VariantsToVCF"));
-        metaData.add("reference=" + this.getToolkit().getArguments().referenceFile.getAbsolutePath());
+        metaData.add(new VCFHeaderLine("reference", this.getToolkit().getArguments().referenceFile.getAbsolutePath()));
 
         Set<String> additionalColumns = new HashSet<String>();
         additionalColumns.add("FORMAT");

java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriterFactory.java

@@ -38,7 +38,7 @@ public class GenotypeWriterFactory {
                                         SAMFileHeader header,
                                         File destination,
                                         Set<String> sampleNames,
-                                        Set<String> headerInfo) {
+                                        Set<VCFHeaderLine> headerInfo) {
         switch (format) {
             case GLF:
                 return new GLFWriter(header.toString(), destination);
@@ -57,7 +57,7 @@ public class GenotypeWriterFactory {
                                         SAMFileHeader header,
                                         PrintStream destination,
                                         Set<String> sampleNames,
-                                        Set<String> headerInfo) {
+                                        Set<VCFHeaderLine> headerInfo) {
         switch (format) {
             case GELI:
                 return new GeliTextWriter(destination);

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFFilterHeaderLine.java

@@ -0,0 +1,40 @@
+package org.broadinstitute.sting.utils.genotype.vcf;
+
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class VCFFilterHeaderLine
+ *         <p/>
+ *         A class representing a key=value entry for FILTER fields in the VCF header
+ */
+public class VCFFilterHeaderLine extends VCFHeaderLine {
+
+    private String mName;
+    private String mDescription;
+
+
+    /**
+     * create a VCF filter header line
+     *
+     * @param name         the name for this header line
+     * @param description  the description for this header line
+     */
+    public VCFFilterHeaderLine(String name, String description) {
+        super("FILTER", "");
+        mName = name;
+        mDescription = description;
+    }
+
+    protected String makeStringRep() {
+        return String.format("FILTER=%s,\"%s\"", mName, mDescription);
+    }
+
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFFilterHeaderLine) )
+            return false;
+        VCFFilterHeaderLine other = (VCFFilterHeaderLine)o;
+        return mName.equals(other.mName) &&
+               mDescription.equals(other.mDescription);
+    }
+}

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFFormatHeaderLine.java

@@ -0,0 +1,53 @@
+package org.broadinstitute.sting.utils.genotype.vcf;
+
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class VCFFormatHeaderLine
+ *         <p/>
+ *         A class representing a key=value entry for genotype FORMAT fields in the VCF header
+ */
+public class VCFFormatHeaderLine extends VCFHeaderLine {
+
+    // the info field types
+    public enum INFO_TYPE {
+        Integer, Float, String
+    }
+
+    private String mName;
+    private int mCount;
+    private String mDescription;
+    private INFO_TYPE mType;
+
+
+    /**
+     * create a VCF format header line
+     *
+     * @param name         the name for this header line
+     * @param count        the count for this header line
+     * @param type         the type for this header line
+     * @param description  the description for this header line
+     */
+    public VCFFormatHeaderLine(String name, int count, INFO_TYPE type, String description) {
+        super("FORMAT", "");
+        mName = name;
+        mCount = count;
+        mType = type;
+        mDescription = description;
+    }
+
+    protected String makeStringRep() {
+        return String.format("FORMAT=%s,%d,%s,\"%s\"", mName, mCount, mType.toString(), mDescription);
+    }
+
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFFormatHeaderLine) )
+            return false;
+        VCFFormatHeaderLine other = (VCFFormatHeaderLine)o;
+        return mName.equals(other.mName) &&
+               mCount == other.mCount &&
+               mDescription.equals(other.mDescription) &&
+               mType == other.mType;
+    }
+}

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java

@@ -262,12 +262,12 @@ public class VCFGenotypeRecord implements Genotype, SampleBacked {
         return result;
     }
 
-    public static Set<String> getSupportedHeaderStrings() {
+    public static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
-        Set<String> result = new HashSet<String>();
+        Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
-        result.add("FORMAT=" + GENOTYPE_KEY + ",1,String,\"Genotype\"");
+        result.add(new VCFFormatHeaderLine(GENOTYPE_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.String, "Genotype"));
-        result.add("FORMAT=" + GENOTYPE_QUALITY_KEY + ",1,Integer,\"Genotype Quality\"");
+        result.add(new VCFFormatHeaderLine(GENOTYPE_QUALITY_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.Integer, "Genotype Quality"));
-        result.add("FORMAT=" + DEPTH_KEY + ",1,Integer,\"Read Depth (without MQ0 reads)\"");
+        result.add(new VCFFormatHeaderLine(DEPTH_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.Integer, "Read Depth (without MQ0 reads)"));
-        //result.add("FORMAT=" + HAPLOTYPE_QUALITY_KEY + ",1,Integer,\"Haplotype Quality\"");
+        //result.add(new VCFFormatHeaderLine(HAPLOTYPE_QUALITY_KEY, 1, VCFFormatHeaderLine.INFO_TYPE.Integer, "Haplotype Quality"));
         return result;
     }
 }

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java

@@ -25,7 +25,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
     protected static Logger logger = Logger.getLogger(VCFGenotypeWriterAdapter.class);
 
 
-    public VCFGenotypeWriterAdapter(File writeTo, Set<String> sampleNames, Set<String> headerInfo) {
+    public VCFGenotypeWriterAdapter(File writeTo, Set<String> sampleNames, Set<VCFHeaderLine> headerInfo) {
         mSampleNames.addAll(sampleNames);
 
         initializeHeader(headerInfo);
@@ -34,7 +34,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
         mWriter = new VCFWriter(mHeader, writeTo);
     }
 
-    public VCFGenotypeWriterAdapter(OutputStream writeTo, Set<String> sampleNames, Set<String> headerInfo) {
+    public VCFGenotypeWriterAdapter(OutputStream writeTo, Set<String> sampleNames, Set<VCFHeaderLine> headerInfo) {
         mSampleNames.addAll(sampleNames);
 
         initializeHeader(headerInfo);
@@ -48,11 +48,11 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
      *
      * @param optionalHeaderInfo the optional header fields
      */
-    private void initializeHeader(Set<String> optionalHeaderInfo) {
+    private void initializeHeader(Set<VCFHeaderLine> optionalHeaderInfo) {
-        Set<String> hInfo = new TreeSet<String>();
+        Set<VCFHeaderLine> hInfo = new TreeSet<VCFHeaderLine>();
 
         // setup the header fields
-        hInfo.add(VCFHeader.FULL_FORMAT_LINE);
+        hInfo.add(new VCFHeaderLine(VCFHeader.FILE_FORMAT_KEY, VCFHeader.VCF_VERSION));
         hInfo.addAll(optionalHeaderInfo);
         
         // setup the sample names

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFHeader.java

@@ -8,12 +8,12 @@ import java.util.*;
  *         <p/>
  *         Class VCFHeader
  *         <p/>
- *         A descriptions should go here. Blame aaron if it's missing.
+ *         A class representing the VCF header
  */
 public class VCFHeader {
 
-    public static final String FILE_FORMAT_KEY = "fileformat=";
+    public static final String FILE_FORMAT_KEY = "fileformat";
-    public static final String OLD_FILE_FORMAT_KEY = "format=";   // from version 3.2
+    public static final String OLD_FILE_FORMAT_KEY = "format";   // from version 3.2
 
 
     /** the current vcf version we support. */
@@ -22,7 +22,6 @@ public class VCFHeader {
     public static final double VCF_VERSION_NUMBER = 3.3;
     public static final String VCF_VERSION = VCF_VERSION_HEADER + VCF_VERSION_NUMBER;
 
-    public static final String FULL_FORMAT_LINE = FILE_FORMAT_KEY + VCF_VERSION;
 
     // the manditory header fields
     public enum HEADER_FIELDS {
@@ -30,7 +29,7 @@ public class VCFHeader {
     }
 
     // the associated meta data
-    private final Set<String> mMetaData;
+    private final Set<VCFHeaderLine> mMetaData;
 
     // the list of auxillary tags
     private final Set<String> mGenotypeSampleNames = new LinkedHashSet<String>();
@@ -50,8 +49,8 @@ public class VCFHeader {
      *
      * @param metaData     the meta data associated with this header
      */
-    public VCFHeader(Set<String> metaData) {
+    public VCFHeader(Set<VCFHeaderLine> metaData) {
-        mMetaData = new TreeSet<String>(metaData);
+        mMetaData = new TreeSet<VCFHeaderLine>(metaData);
         checkVCFVersion();
     }
 
@@ -61,8 +60,8 @@ public class VCFHeader {
      * @param metaData            the meta data associated with this header
      * @param genotypeSampleNames the genotype format field, and the sample names
      */
-    public VCFHeader(Set<String> metaData, Set<String> genotypeSampleNames) {
+    public VCFHeader(Set<VCFHeaderLine> metaData, Set<String> genotypeSampleNames) {
-        mMetaData = new TreeSet<String>(metaData);
+        mMetaData = new TreeSet<VCFHeaderLine>(metaData);
         for (String col : genotypeSampleNames) {
             if (!col.equals("FORMAT"))
                 mGenotypeSampleNames.add(col);
@@ -77,19 +76,15 @@ public class VCFHeader {
      */
     public void checkVCFVersion() {
         String version = null;
-        for ( String field : mMetaData ) {
+        for ( VCFHeaderLine line : mMetaData ) {
-            if ( field.startsWith(FILE_FORMAT_KEY) ) {
+            if ( line.getKey().equals(FILE_FORMAT_KEY) || line.getKey().equals(OLD_FILE_FORMAT_KEY) ) {
-                version = field.substring(FILE_FORMAT_KEY.length());
+                version = line.getValue();
-                break;
-            }
-            else if ( field.startsWith(OLD_FILE_FORMAT_KEY) ) {
-                version = field.substring(OLD_FILE_FORMAT_KEY.length());
                 break;
             }
         }
 
         if ( version == null )
-            mMetaData.add(FULL_FORMAT_LINE);
+            mMetaData.add(new VCFHeaderLine(FILE_FORMAT_KEY, VCF_VERSION));
         else if ( !isSupportedVersion(version) )
             throw new RuntimeException("VCF version " + version +
                     " is not yet supported; only version " + VCF_VERSION + " and earlier can be used");
@@ -124,7 +119,7 @@ public class VCFHeader {
      *
      * @return a set of the meta data
      */
-    public Set<String> getMetaData() {
+    public Set<VCFHeaderLine> getMetaData() {
         return mMetaData;
     }
 

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderLine.java

@@ -0,0 +1,86 @@
+package org.broadinstitute.sting.utils.genotype.vcf;
+
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class VCFHeaderLine
+ *         <p/>
+ *         A class representing a key=value entry in the VCF header
+ */
+public class VCFHeaderLine implements Comparable {
+
+    private String stringRep = null;
+    private String mKey = null;
+    private String mValue = null;
+
+
+    /**
+     * create a VCF header line
+     *
+     * @param key     the key for this header line
+     * @param value   the value for this header line
+     */
+    public VCFHeaderLine(String key, String value) {
+        mKey = key;
+        mValue = value;
+    }
+
+    /**
+     * Get the key
+     *
+     * @return the key
+     */
+    public String getKey() {
+        return mKey;
+    }
+
+    /**
+     * Set the key
+     *
+     * @param key     the key for this header line
+     */
+    public void setKey(String key) {
+        mKey = key;
+        stringRep = null;
+    }
+
+    /**
+     * Get the value
+     *
+     * @return the value
+     */
+    public String getValue() {
+        return mValue;
+    }
+
+    /**
+     * Set the value
+     *
+     * @param value     the value for this header line
+     */
+    public void setValue(String value) {
+        mValue = value;
+        stringRep = null;
+    }
+
+    public String toString() {
+        if ( stringRep == null )
+            stringRep = makeStringRep();
+        return stringRep;
+    }
+
+    protected String makeStringRep() {
+        return mKey + "=" + mValue;
+    }
+
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFHeaderLine) )
+            return false;
+        return mKey.equals(((VCFHeaderLine)o).getKey()) && mValue.equals(((VCFHeaderLine)o).getValue());
+    }
+
+    public int compareTo(Object other) {
+        return toString().compareTo(other.toString());
+    }
+}

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFInfoHeaderLine.java

@@ -0,0 +1,53 @@
+package org.broadinstitute.sting.utils.genotype.vcf;
+
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class VCFInfoHeaderLine
+ *         <p/>
+ *         A class representing a key=value entry for INFO fields in the VCF header
+ */
+public class VCFInfoHeaderLine extends VCFHeaderLine {
+
+    // the info field types
+    public enum INFO_TYPE {
+        Integer, Float, String
+    }
+
+    private String mName;
+    private int mCount;
+    private String mDescription;
+    private INFO_TYPE mType;
+
+
+    /**
+     * create a VCF info header line
+     *
+     * @param name         the name for this header line
+     * @param count        the count for this header line
+     * @param type         the type for this header line
+     * @param description  the description for this header line
+     */
+    public VCFInfoHeaderLine(String name, int count, INFO_TYPE type, String description) {
+        super("INFO", "");
+        mName = name;
+        mCount = count;
+        mType = type;
+        mDescription = description;
+    }
+
+    protected String makeStringRep() {
+        return String.format("INFO=%s,%d,%s,\"%s\"", mName, mCount, mType.toString(), mDescription);
+    }
+
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFInfoHeaderLine) )
+            return false;
+        VCFInfoHeaderLine other = (VCFInfoHeaderLine)o;
+        return mName.equals(other.mName) &&
+               mCount == other.mCount &&
+               mDescription.equals(other.mDescription) &&
+               mType == other.mType;
+    }
+}

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java

@@ -146,7 +146,7 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
      * @return a VCF Header created from the list of stinrgs
      */
     protected VCFHeader createHeader(List<String> headerStrings) {
-        Set<String> metaData = new TreeSet<String>();
+        Set<VCFHeaderLine> metaData = new TreeSet<VCFHeaderLine>();
         Set<String> auxTags = new LinkedHashSet<String>();
         // iterate over all the passed in strings
         for ( String str : headerStrings ) {
@@ -169,7 +169,9 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
                     arrayIndex++;
                 }
             } else {
-                metaData.add(str.substring(2));
+                int equals = str.indexOf("=");
+                if ( equals != -1 )
+                    metaData.add(new VCFHeaderLine(str.substring(2, equals), str.substring(equals+1)));
             }
         }
 

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java

@@ -27,10 +27,10 @@ public class VCFUtils {
      *
      * @return a set of all fields
      */
-    public static Set<String> getHeaderFields(GenomeAnalysisEngine toolkit) {
+    public static Set<VCFHeaderLine> getHeaderFields(GenomeAnalysisEngine toolkit) {
 
         // keep a map of sample name to occurrences encountered
-        TreeSet<String> fields = new TreeSet<String>();
+        TreeSet<VCFHeaderLine> fields = new TreeSet<VCFHeaderLine>();
 
         // iterate to get all of the sample names
         List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java

@@ -50,23 +50,21 @@ public class VCFWriter {
                 new OutputStreamWriter(location));
         try {
             // the fileformat field needs to be written first
-            TreeSet<String> allMetaData = new TreeSet<String>(header.getMetaData());
+            TreeSet<VCFHeaderLine> nonFormatMetaData = new TreeSet<VCFHeaderLine>();
-            for ( String metadata : allMetaData ) {
+            for ( VCFHeaderLine line : header.getMetaData() ) {
-                if ( metadata.startsWith(VCFHeader.FILE_FORMAT_KEY) ) {
+                if ( line.getKey().equals(VCFHeader.FILE_FORMAT_KEY) ) {
-                    mWriter.write(VCFHeader.METADATA_INDICATOR + metadata + "\n");
+                    mWriter.write(VCFHeader.METADATA_INDICATOR + line.toString() + "\n");
-                    break;
                 }
-                else if ( metadata.startsWith(VCFHeader.OLD_FILE_FORMAT_KEY) ) {
+                else if ( line.getKey().equals(VCFHeader.OLD_FILE_FORMAT_KEY) ) {
-                    mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeader.FILE_FORMAT_KEY + metadata.substring(VCFHeader.OLD_FILE_FORMAT_KEY.length()) + "\n");
+                    mWriter.write(VCFHeader.METADATA_INDICATOR + VCFHeader.FILE_FORMAT_KEY + line.toString().substring(VCFHeader.OLD_FILE_FORMAT_KEY.length()) + "\n");
-                    break;
+                } else {
+                    nonFormatMetaData.add(line);
                 }
             }
 
             // write the rest of the header meta-data out
-            for ( String metadata : header.getMetaData() ) {
+            for ( VCFHeaderLine line : nonFormatMetaData )
-                if ( !metadata.startsWith(VCFHeader.FILE_FORMAT_KEY) && !metadata.startsWith(VCFHeader.OLD_FILE_FORMAT_KEY) )
+                mWriter.write(VCFHeader.METADATA_INDICATOR + line + "\n");
-                    mWriter.write(VCFHeader.METADATA_INDICATOR + metadata + "\n");                
-            }
 
             // write out the column line
             StringBuilder b = new StringBuilder();

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderTest.java

@@ -17,8 +17,7 @@ import java.util.*;
  */
 public class VCFHeaderTest extends BaseTest {
 
-    private Set<VCFHeader.HEADER_FIELDS> headerFields = new LinkedHashSet<VCFHeader.HEADER_FIELDS>();
+    private Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
-    private Set<String> metaData = new HashSet();
     private Set<String> additionalColumns = new HashSet<String>();
 
     /**
@@ -26,8 +25,8 @@ public class VCFHeaderTest extends BaseTest {
      */
     @Test
     public void testHeaderConstructor() {
-        metaData.add(VCFHeader.FULL_FORMAT_LINE); // required
+        metaData.add(new VCFHeaderLine(VCFHeader.FILE_FORMAT_KEY, VCFHeader.VCF_VERSION));
-        metaData.add("two=2");
+        metaData.add(new VCFHeaderLine("two", "2"));
         additionalColumns.add("extra1");
         additionalColumns.add("extra2");
         // this should create a header that is valid

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java

@@ -24,17 +24,16 @@ public class VCFReaderTest extends BaseTest {
     private static final File complexFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/complexExample.vcf");
     private static final File headerNoRecordsFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/headerNoRecords.vcf");
     
-    private static IndexedFastaSequenceFile seq;
 
-       @BeforeClass
+    @BeforeClass
-       public static void beforeTests() {
+    public static void beforeTests() {
-           try {
+        try {
-               seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta"));
+            IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta"));
-           } catch (FileNotFoundException e) {
+            GenomeLocParser.setupRefContigOrdering(seq);
-               throw new StingException("unable to load the sequence dictionary");
+        } catch (FileNotFoundException e) {
-           }
+            throw new StingException("unable to load the sequence dictionary");
-           GenomeLocParser.setupRefContigOrdering(seq);
+        }
-       }
+    }
 
     @Test
     public void testVCFInput() {
@@ -330,7 +329,6 @@ public class VCFReaderTest extends BaseTest {
     public void testHeaderNoRecords() {
         VCFReader reader = new VCFReader(headerNoRecordsFile);
         Assert.assertTrue(reader.getHeader().getMetaData() != null);
-        Iterator<VCFRecord> iter = reader.iterator();
         Assert.assertTrue(!reader.iterator().hasNext());
 
     }

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFRecordTest.java

@@ -22,21 +22,20 @@ import java.io.FileNotFoundException;
  */
 public class VCFRecordTest extends BaseTest {
 
-    private static IndexedFastaSequenceFile seq;
-
     @BeforeClass
     public static void beforeTests() {
         try {
-            seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+            IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+            GenomeLocParser.setupRefContigOrdering(seq);
         } catch (FileNotFoundException e) {
             throw new StingException("unable to load the sequence dictionary");
         }
-        GenomeLocParser.setupRefContigOrdering(seq);
     }
 
     /**
      * create a fake VCF record
      *
+     * @param infoFields  the info fields
      * @return a VCFRecord
      */
     private static VCFRecord makeFakeVCFRecord(Map<String, String> infoFields) {
@@ -140,9 +139,9 @@ public class VCFRecordTest extends BaseTest {
      * @return a fake VCF header
      */
     public static VCFHeader createFakeHeader() {
-        Set<String> metaData = new HashSet();
+        Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
-        metaData.add(VCFHeader.FULL_FORMAT_LINE); // required
+        metaData.add(new VCFHeaderLine(VCFHeader.FILE_FORMAT_KEY, VCFHeader.VCF_VERSION));
-        metaData.add("two=2");
+        metaData.add(new VCFHeaderLine("two", "2"));
         Set<String> additionalColumns = new HashSet<String>();
         additionalColumns.add("FORMAT");
         additionalColumns.add("sample1");
@@ -158,8 +157,6 @@ public class VCFRecordTest extends BaseTest {
         Map<String, String> infoFields = new HashMap<String, String>();
         infoFields.put("DP", "50");
         VCFRecord rec = makeFakeVCFRecord(infoFields);
-        Map<String, String> metaData = new HashMap<String, String>();
-        List<String> additionalColumns = new ArrayList<String>();
         String rep = rec.toStringEncoding(createFakeHeader());
         Assert.assertTrue(stringRep.equals(rep));
         rec.addInfoField("AB", "CD");

java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterTest.java

@@ -21,21 +21,18 @@ import java.util.*;
  *         This class tests out the ability of the VCF writer to correctly write VCF files
  */
 public class VCFWriterTest extends BaseTest {
-    private Set<VCFHeader.HEADER_FIELDS> headerFields = new LinkedHashSet<VCFHeader.HEADER_FIELDS>();
+    private Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
-    private Set<String> metaData = new HashSet();
     private Set<String> additionalColumns = new HashSet<String>();
     private File fakeVCFFile = new File("FAKEVCFFILEFORTESTING.vcf");
 
-    private static IndexedFastaSequenceFile seq;
-
     @BeforeClass
     public static void beforeTests() {
         try {
-            seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+            IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+            GenomeLocParser.setupRefContigOrdering(seq);
         } catch (FileNotFoundException e) {
             throw new StingException("unable to load the sequence dictionary");
         }
-        GenomeLocParser.setupRefContigOrdering(seq);
     }
 
     /** test, using the writer and reader, that we can output and input a VCF file without problems */
@@ -50,7 +47,7 @@ public class VCFWriterTest extends BaseTest {
         int counter = 0;
         // validate what we're reading in
         validateHeader(reader.getHeader());
-        for(VCFRecord rec :reader) {
+        for (VCFRecord rec : reader) {
             counter++;
         }
         Assert.assertEquals(2,counter);
@@ -60,11 +57,13 @@ public class VCFWriterTest extends BaseTest {
 
     /**
      * create a fake header of known quantity
+     * @param metaData           the header lines
+     * @param additionalColumns  the additional column names
      * @return a fake VCF header
      */
-    public static VCFHeader createFakeHeader(Set<String> metaData, Set<String> additionalColumns) {
+    public static VCFHeader createFakeHeader(Set<VCFHeaderLine> metaData, Set<String> additionalColumns) {
-        metaData.add(VCFHeader.FULL_FORMAT_LINE); // required
+        metaData.add(new VCFHeaderLine(VCFHeader.FILE_FORMAT_KEY, VCFHeader.VCF_VERSION));
-        metaData.add("two=2");
+        metaData.add(new VCFHeaderLine("two", "2"));
         additionalColumns.add("FORMAT");
         additionalColumns.add("extra1");
         additionalColumns.add("extra2");