Minor interface change for VCFGenotypeRecord.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2537 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -137,16 +137,18 @@ public class VariantsToVCF extends RefWalker<Integer, Integer> {
                 str.put("GQ", lod);
                 if (depth > 0) str.put("DP", String.valueOf(depth));
 
-                gt.add(new VCFGenotypeRecord(name, alleles, VCFGenotypeRecord.PHASE.UNPHASED, str));
+                VCFGenotypeRecord rec = new VCFGenotypeRecord(name, alleles, VCFGenotypeRecord.PHASE.UNPHASED);
+                for ( Map.Entry<String, String> entry : str.entrySet() )
+                    rec.setField(entry.getKey(), entry.getValue());
+                gt.add(rec);
 
                 numSNPs++;
                 snpQual += av.getNegLog10PError();
             } else if (BaseUtils.simpleBaseToBaseIndex(ref.getBase()) != -1) {
-                Map<String, String> str = new HashMap<String, String>();
                 List<VCFGenotypeEncoding> alleles = new ArrayList<VCFGenotypeEncoding>();
                 alleles.add(new VCFGenotypeEncoding(String.valueOf(ref.getBase())));
                 alleles.add(new VCFGenotypeEncoding(String.valueOf(ref.getBase())));
-                gt.add(new VCFGenotypeRecord(name, alleles, VCFGenotypeRecord.PHASE.UNPHASED, str));
+                gt.add(new VCFGenotypeRecord(name, alleles, VCFGenotypeRecord.PHASE.UNPHASED));
 
                 numRefs++;
             }

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

@@ -58,20 +58,12 @@ public class VCFGenotypeRecord implements Genotype, SampleBacked {
      * @param sampleName  sample name
      * @param genotypes   list of genotypes
      * @param phasing     phasing
-     * @param otherFlags  other flags
      */
-    public VCFGenotypeRecord(String sampleName, List<VCFGenotypeEncoding> genotypes, PHASE phasing, Map<String, String> otherFlags) {
+    public VCFGenotypeRecord(String sampleName, List<VCFGenotypeEncoding> genotypes, PHASE phasing) {
         mSampleName = sampleName;
-        if (genotypes != null) this.mGenotypeAlleles.addAll(genotypes);
+        if (genotypes != null)
+            this.mGenotypeAlleles.addAll(genotypes);
         mPhaseType = phasing;
-        if (otherFlags != null) {
-            // we need to be backwards compatible
-            if ( otherFlags.containsKey(OLD_DEPTH_KEY) ) {
-                otherFlags.put(DEPTH_KEY, otherFlags.get(OLD_DEPTH_KEY));
-                otherFlags.remove(OLD_DEPTH_KEY);
-            }
-            mFields.putAll(otherFlags);
-        }
     }
 
     public void setVCFRecord(VCFRecord record) {
@@ -82,6 +74,23 @@ public class VCFGenotypeRecord implements Genotype, SampleBacked {
         mSampleName = name;
     }
 
+    /**
+     * Adds a field to the genotype record.
+     * Throws an exception if the key is GT, as that's computed internally.
+     *
+     * @param key    the field name (use static variables above for common fields)
+     * @param value  the field value
+     */
+    public void setField(String key, String value) {
+        // make sure the GT field isn't being set
+        if ( key.equals(GENOTYPE_KEY) )
+            throw new IllegalArgumentException("Setting the GT field is not allowed as that's done internally");
+        // we need to be backwards compatible
+        if ( key.equals(OLD_DEPTH_KEY) )
+             key = DEPTH_KEY;
+        mFields.put(key, value);
+    }
+
     /**
      * determine the phase of the genotype
      *
@@ -217,7 +226,8 @@ public class VCFGenotypeRecord implements Genotype, SampleBacked {
 
     }
 
-    @Override public String toString() {
+    @Override
+    public String toString() {
         return String.format("[VCFGenotype %s %s %s %s]", getLocation(), mSampleName, this.mGenotypeAlleles, mFields);
     }
 

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

@@ -192,18 +192,12 @@ public class VCFGenotypeWriterAdapter implements VCFGenotypeWriter {
      * @return a VCFGenotypeRecord for the no call situation
      */
     private VCFGenotypeRecord createNoCallRecord(String sampleName) {
-        Map<String, String> map = new HashMap<String, String>();
-
 
         List<VCFGenotypeEncoding> alleles = new ArrayList<VCFGenotypeEncoding>();
         alleles.add(new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE));
         alleles.add(new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE));
 
-        VCFGenotypeRecord record = new VCFGenotypeRecord(sampleName,
+        return new VCFGenotypeRecord(sampleName, alleles, VCFGenotypeRecord.PHASE.UNPHASED);
-                                                         alleles,
-                                                         VCFGenotypeRecord.PHASE.UNPHASED,
-                                                         map);
-        return record;
     }
 
     /** @return true if we support multisample, false otherwise */

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

@@ -256,7 +256,7 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
      */
     public static VCFGenotypeRecord getVCFGenotype(String sampleName, String[] keyStrings, String genotypeString, String altAlleles[], char referenceBase) {
         // parameters to create the VCF genotype record
-        Map<String, String> tagToValue = new HashMap<String, String>();
+        HashMap<String, String> tagToValue = new HashMap<String, String>();
         VCFGenotypeRecord.PHASE phase = VCFGenotypeRecord.PHASE.UNKNOWN;
         List<VCFGenotypeEncoding> bases = new ArrayList<VCFGenotypeEncoding>();
 
@@ -294,7 +294,11 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
         else if ( genotypeString.length() > 0 )
             throw new RuntimeException("VCFReader: genotype string contained additional unprocessed fields: " + genotypeString
                     + ".  This most likely means that the format string is shorter then the value fields.");
-        return new VCFGenotypeRecord(sampleName, bases, phase, tagToValue);
+
+        VCFGenotypeRecord rec = new VCFGenotypeRecord(sampleName, bases, phase);
+        for ( Map.Entry<String, String> entry : tagToValue.entrySet() )
+            rec.setField(entry.getKey(), entry.getValue());
+        return rec;
     }
 
 

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

@@ -210,24 +210,21 @@ public class VCFUtils {
      * @return a VCFGenotypeRecord
      */
     public static VCFGenotypeRecord createVCFGenotypeRecord(VCFParameters params, VCFGenotypeRecord gtype, VCFRecord vcfrecord) {
-        Map<String, String> map = new HashMap<String, String>();
-
-        // calculate the genotype quality and the read depth
-        map.put(VCFGenotypeRecord.DEPTH_KEY, String.valueOf(gtype.getReadCount()));
-        params.addFormatItem(VCFGenotypeRecord.DEPTH_KEY);
-        double qual = Math.min(10.0 * gtype.getNegLog10PError(), VCFGenotypeRecord.MAX_QUAL_VALUE);
-        map.put(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%.2f", qual));
-        params.addFormatItem(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
 
         List<VCFGenotypeEncoding> alleles = createAlleleArray(gtype);
         for (VCFGenotypeEncoding allele : alleles) {
             params.addAlternateBase(allele);
         }
 
-        VCFGenotypeRecord record = new VCFGenotypeRecord(gtype.getSampleName(),
+        VCFGenotypeRecord record = new VCFGenotypeRecord(gtype.getSampleName(), alleles, VCFGenotypeRecord.PHASE.UNPHASED);
-                                                         alleles,
+
-                                                         VCFGenotypeRecord.PHASE.UNPHASED,
+        // calculate the genotype quality and the read depth
-                                                         map);
+        record.setField(VCFGenotypeRecord.DEPTH_KEY, String.valueOf(gtype.getReadCount()));
+        params.addFormatItem(VCFGenotypeRecord.DEPTH_KEY);
+        double qual = Math.min(10.0 * gtype.getNegLog10PError(), VCFGenotypeRecord.MAX_QUAL_VALUE);
+        record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%.2f", qual));
+        params.addFormatItem(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
+
         record.setVCFRecord(vcfrecord);
         return record;
     }
@@ -241,24 +238,21 @@ public class VCFUtils {
      * @return a VCFGenotypeRecord
      */
     public static VCFGenotypeRecord createVCFGenotypeRecord(VCFParameters params, VCFGenotypeCall gtype) {
-        Map<String, String> map = new HashMap<String, String>();
-
-        // calculate the RMS mapping qualities and the read depth
-        map.put(VCFGenotypeRecord.DEPTH_KEY, String.valueOf(gtype.getReadCount()));
-        params.addFormatItem(VCFGenotypeRecord.DEPTH_KEY);
-        double qual = Math.min(10.0 * gtype.getNegLog10PError(), VCFGenotypeRecord.MAX_QUAL_VALUE);
-        map.put(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%.2f", qual));
-        params.addFormatItem(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
 
         List<VCFGenotypeEncoding> alleles = createAlleleArray(gtype);
         for (VCFGenotypeEncoding allele : alleles) {
             params.addAlternateBase(allele);
         }
 
-        VCFGenotypeRecord record = new VCFGenotypeRecord(gtype.getSampleName(),
+        VCFGenotypeRecord record = new VCFGenotypeRecord(gtype.getSampleName(), alleles, VCFGenotypeRecord.PHASE.UNPHASED);
-                                                         alleles,
+
-                                                         VCFGenotypeRecord.PHASE.UNPHASED,
+        // calculate the RMS mapping qualities and the read depth
-                                                         map);
+        record.setField(VCFGenotypeRecord.DEPTH_KEY, String.valueOf(gtype.getReadCount()));
+        params.addFormatItem(VCFGenotypeRecord.DEPTH_KEY);
+        double qual = Math.min(10.0 * gtype.getNegLog10PError(), VCFGenotypeRecord.MAX_QUAL_VALUE);
+        record.setField(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY, String.format("%.2f", qual));
+        params.addFormatItem(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY);
+
         return record;
     }
 

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

@@ -56,12 +56,12 @@ public class VCFRecordTest extends BaseTest {
      * @return a VCFGenotypeRecord
      */
     private static VCFGenotypeRecord createGenotype(String name, String Allele1, String Allele2) {
-        Map<String, String> keyValues = new HashMap<String, String>();
-        keyValues.put("AA", "2");
         List<VCFGenotypeEncoding> Alleles = new ArrayList<VCFGenotypeEncoding>();
         Alleles.add(new VCFGenotypeEncoding(Allele1));
         Alleles.add(new VCFGenotypeEncoding(Allele2));
-        return new VCFGenotypeRecord(name, Alleles, VCFGenotypeRecord.PHASE.PHASED, keyValues);
+        VCFGenotypeRecord rec = new VCFGenotypeRecord(name, Alleles, VCFGenotypeRecord.PHASE.PHASED);
+        rec.setField("AA", "2");
+        return rec;
     }
 
     @Test

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

@@ -85,13 +85,12 @@ public class VCFWriterTest extends BaseTest {
 
         List<VCFGenotypeRecord> gt = new ArrayList<VCFGenotypeRecord>();
         for (String name : header.getGenotypeSamples()) {
-            Map<String,String> str = new HashMap<String,String>();
-            str.put("bb","0");
-
             List<VCFGenotypeEncoding> myAlleles = new ArrayList<VCFGenotypeEncoding>();
             myAlleles.add(new VCFGenotypeEncoding("C"));
             myAlleles.add(new VCFGenotypeEncoding("D1"));
-            gt.add(new VCFGenotypeRecord(name, myAlleles, VCFGenotypeRecord.PHASE.PHASED, str));
+            VCFGenotypeRecord rec = new VCFGenotypeRecord(name, myAlleles, VCFGenotypeRecord.PHASE.PHASED);
+            rec.setField("bb", "0");
+            gt.add(rec);
         }
         return new VCFRecord('A',"chr1",1,"RANDOM",altBases,0,".",infoFields, "GT:AA",gt);