Adding support for other simple header line types (e.g. ALT) and cleaning up the interface a bit.

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
@@ -41,8 +42,8 @@ import java.util.*;
 public class ChromosomeCounts implements InfoFieldAnnotation, StandardAnnotation {
 
     private String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
-    private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, -1, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
+    private VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"),
-            new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, -1, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
+            new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"),
             new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes") };
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {

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

@@ -37,7 +37,6 @@ import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import java.util.*;
 import java.io.PrintStream;
@@ -158,7 +157,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         }
 
         // FORMAT and INFO fields
-        headerInfo.addAll(VCFUtils.getSupportedHeaderStrings());
+        headerInfo.addAll(getSupportedHeaderStrings());
 
         // FILTER fields
         if ( UAC.STANDARD_CONFIDENCE_FOR_EMITTING < UAC.STANDARD_CONFIDENCE_FOR_CALLING )
@@ -167,6 +166,20 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         return headerInfo;
     }
 
+    /**
+     * return a set of supported format lines; what we currently support for output in the genotype fields of a VCF
+     * @return a set of VCF format lines
+     */
+    private static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
+        Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
+        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
+        result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2"));
+
+        return result;
+    }
+
     /**
      * Compute at a given locus.
      *

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java

@@ -358,9 +358,8 @@ public class StandardVCFWriter implements VCFWriter {
             mWriter.write(key);
 
             if ( !entry.getValue().equals("") ) {
-                int numVals = 1;
                 VCFInfoHeaderLine metaData = mHeader.getInfoHeaderLine(key);
-                if ( metaData != null && (metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() > 0) ) {
+                if ( metaData == null || metaData.getCountType() != VCFHeaderLineCount.INTEGER || metaData.getCount() != 0 ) {
                     mWriter.write("=");
                     mWriter.write(entry.getValue());
                 }

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFAltHeaderLine.java

@@ -0,0 +1,28 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+/**
+ * @author ebanks
+ * A class representing a key=value entry for ALT fields in the VCF header
+ */
+public class VCFAltHeaderLine extends VCFSimpleHeaderLine  {
+
+    /**
+     * create a VCF filter header line
+     *
+     * @param name         the name for this header line
+     * @param description  the description for this header line
+     */
+    public VCFAltHeaderLine(String name, String description) {
+        super(name, description, SupportedHeaderLineType.ALT);
+    }
+
+    /**
+     * create a VCF info header line
+     *
+     * @param line      the header line
+     * @param version   the vcf header version
+     */
+    protected VCFAltHeaderLine(String line, VCFHeaderVersion version) {
+        super(line, version, SupportedHeaderLineType.ALT);
+    }
+}

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java

@@ -89,6 +89,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
      * @param count        the count for this header line
      * @param type         the type for this header line
      * @param description  the description for this header line
+     * @param lineType     the header line type
      */
     protected VCFCompoundHeaderLine(String name, int count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
         super(lineType.toString(), "");
@@ -108,6 +109,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
      * @param count        the count type for this header line
      * @param type         the type for this header line
      * @param description  the description for this header line
+     * @param lineType     the header line type
      */
     protected VCFCompoundHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description, SupportedHeaderLineType lineType) {
         super(lineType.toString(), "");
@@ -124,6 +126,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
      *
      * @param line   the header line
      * @param version      the VCF header version
+     * @param lineType     the header line type
      *
      */
     protected VCFCompoundHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java

@@ -1,19 +1,10 @@
 package org.broadinstitute.sting.utils.codecs.vcf;
 
-import java.util.Arrays;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
-
 /**
  * @author ebanks
  * A class representing a key=value entry for FILTER fields in the VCF header
  */
-public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine  {
+public class VCFFilterHeaderLine extends VCFSimpleHeaderLine  {
-
-    private String name;
-    private String description;
-
 
     /**
      * create a VCF filter header line
@@ -22,12 +13,7 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
      * @param description  the description for this header line
      */
     public VCFFilterHeaderLine(String name, String description) {
-        super("FILTER", "");
+        super(name, description, SupportedHeaderLineType.FILTER);
-        this.name = name;
-        this.description = description;
-
-        if ( name == null || description == null )
-            throw new IllegalArgumentException(String.format("Invalid VCFCompoundHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
     }
 
     /**
@@ -37,34 +23,6 @@ public class VCFFilterHeaderLine extends VCFHeaderLine implements VCFNamedHeader
      * @param version   the vcf header version
      */
     protected VCFFilterHeaderLine(String line, VCFHeaderVersion version) {
-        super("FILTER", "");
+        super(line, version, SupportedHeaderLineType.FILTER);
-        Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
-        name = mapping.get("ID");
-        description = mapping.get("Description");
-        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided 
-            description = UNBOUND_DESCRIPTION;
-    }
-
-    protected String toStringEncoding() {
-        Map<String,Object> map = new LinkedHashMap<String,Object>();
-        map.put("ID", name);
-        map.put("Description", description);
-        return "FILTER=" + VCFHeaderLine.toStringEncoding(map);
-    }
-
-    public boolean equals(Object o) {
-        if ( !(o instanceof VCFFilterHeaderLine) )
-            return false;
-        VCFFilterHeaderLine other = (VCFFilterHeaderLine)o;
-        return name.equals(other.name) &&
-               description.equals(other.description);
-    }
-
-    public String getName() {
-        return name;
-    }
-
-    public String getDescription() {
-        return description;
     }
 }

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java

@@ -17,7 +17,7 @@ public class VCFFormatHeaderLine extends VCFCompoundHeaderLine {
     }
 
     public VCFFormatHeaderLine(String name, VCFHeaderLineCount count, VCFHeaderLineType type, String description) {
-        super(name, count, type, description, SupportedHeaderLineType.INFO);
+        super(name, count, type, description, SupportedHeaderLineType.FORMAT);
     }
 
     protected VCFFormatHeaderLine(String line, VCFHeaderVersion version) {

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java

@@ -0,0 +1,81 @@
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+import java.util.Arrays;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+
+/**
+ * @author ebanks
+ * A class representing a key=value entry for simple VCF header types
+ */
+public abstract class VCFSimpleHeaderLine extends VCFHeaderLine implements VCFNamedHeaderLine  {
+
+    public enum SupportedHeaderLineType {
+        FILTER, ALT;
+    }
+
+    private String name;
+    private String description;
+
+    // our type of line, i.e. filter, alt, etc
+    private final SupportedHeaderLineType lineType;
+
+
+    /**
+     * create a VCF filter header line
+     *
+     * @param name         the name for this header line
+     * @param description  the description for this header line
+     * @param lineType     the header line type
+     */
+    public VCFSimpleHeaderLine(String name, String description, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        this.lineType = lineType;
+        this.name = name;
+        this.description = description;
+
+        if ( name == null || description == null )
+            throw new IllegalArgumentException(String.format("Invalid VCFSimpleHeaderLine: key=%s name=%s desc=%s", super.getKey(), name, description ));
+    }
+
+    /**
+     * create a VCF info header line
+     *
+     * @param line      the header line
+     * @param version   the vcf header version
+     * @param lineType     the header line type
+     */
+    protected VCFSimpleHeaderLine(String line, VCFHeaderVersion version, SupportedHeaderLineType lineType) {
+        super(lineType.toString(), "");
+        this.lineType = lineType;
+        Map<String,String> mapping = VCFHeaderLineTranslator.parseLine(version,line, Arrays.asList("ID","Description"));
+        name = mapping.get("ID");
+        description = mapping.get("Description");
+        if ( description == null && ALLOW_UNBOUND_DESCRIPTIONS ) // handle the case where there's no description provided 
+            description = UNBOUND_DESCRIPTION;
+    }
+
+    protected String toStringEncoding() {
+        Map<String,Object> map = new LinkedHashMap<String,Object>();
+        map.put("ID", name);
+        map.put("Description", description);
+        return lineType.toString() + "=" + VCFHeaderLine.toStringEncoding(map);
+    }
+
+    public boolean equals(Object o) {
+        if ( !(o instanceof VCFSimpleHeaderLine) )
+            return false;
+        VCFSimpleHeaderLine other = (VCFSimpleHeaderLine)o;
+        return name.equals(other.name) &&
+               description.equals(other.description);
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+}

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java

@@ -180,19 +180,4 @@ public class VCFUtils {
 
         return new HashSet<VCFHeaderLine>(map.values());
     }
-
-    /**
-     * return a set of supported format lines; what we currently support for output in the genotype fields of a VCF
-     * @return a set of VCF format lines
-     */
-    public static Set<VCFFormatHeaderLine> getSupportedHeaderStrings() {
-        Set<VCFFormatHeaderLine> result = new HashSet<VCFFormatHeaderLine>();
-        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
-        result.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, -1, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; if site is not biallelic, number of likelihoods if n*(n+1)/2"));
-
-        return result;
-    }
-    
 }