-VCF writer now checks whether the allele frequency has been set before trying to write it out.

-Renamed methods to be more consistent.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2214 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -78,7 +78,7 @@ public abstract class EMGenotypeCalculationModel extends GenotypeCalculationMode
 
                 ((SLODBacked)locusdata).setSLOD(strandScore);
             }
-            locusdata.setAlleleFrequency(overall.getMAF());
+            locusdata.setNonRefAlleleFrequency(overall.getMAF());
         }
         return new Pair<List<Genotype>, GenotypeLocusData>(genotypeCallsFromGenotypeLikelihoods(overall, ref, contexts), locusdata);
     }

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

@@ -323,7 +323,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
         GenotypeLocusData locusdata = GenotypeWriterFactory.createSupportedGenotypeLocusData(OUTPUT_FORMAT, ref, loc, VARIANT_TYPE.SNP);
         if ( locusdata != null ) {
             locusdata.addAlternateAllele(bestAlternateAllele.toString());
-            locusdata.setAlleleFrequency((double)bestAFguess / (double)(frequencyEstimationPoints-1));
+            locusdata.setNonRefAlleleFrequency((double)bestAFguess / (double)(frequencyEstimationPoints-1));
             if ( locusdata instanceof ConfidenceBacked ) {
                 ((ConfidenceBacked)locusdata).setConfidence(phredScaledConfidence);
             }

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

@@ -16,10 +16,16 @@ public interface GenotypeLocusData extends Variation {
      */
     public void addAlternateAllele(String alt);
 
+    /**
+     *
+     * @return true if the allele frequency has been set
+     */
+    public boolean hasNonRefAlleleFrequency();
+
     /**
      *
      * @param   frequency    the allele frequency for this genotype
      */
-    public void setAlleleFrequency(double frequency);
+    public void setNonRefAlleleFrequency(double frequency);
 
 }

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

@@ -21,7 +21,7 @@ public class VCFGenotypeLocusData implements GenotypeLocusData, ConfidenceBacked
     private Double mSLOD = null;
 
     // the allele frequency field
-    private double mAlleleFrequency = 0.0;
+    private double mAlleleFrequency = -1.0;
 
     // the location
     private GenomeLoc mLoc;
@@ -97,6 +97,10 @@ public class VCFGenotypeLocusData implements GenotypeLocusData, ConfidenceBacked
         return mType;
     }
 
+    public boolean hasNonRefAlleleFrequency() {
+        return mAlleleFrequency >= 0.0;
+    }
+
     public double getNonRefAlleleFrequency() {
         return mAlleleFrequency;
     }
@@ -171,7 +175,7 @@ public class VCFGenotypeLocusData implements GenotypeLocusData, ConfidenceBacked
      *
      * @param   frequency    the allele frequency for this genotype
      */
-    public void setAlleleFrequency(double frequency) {
+    public void setNonRefAlleleFrequency(double frequency) {
         mAlleleFrequency = frequency;
     }
 

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

@@ -190,7 +190,8 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
         if ( locusdata != null ) {
             if ( locusdata.getSLOD() != null )
                 infoFields.put("SB", String.format("%.2f", locusdata.getSLOD()));
-            infoFields.put("AF", String.format("%.2f", locusdata.getNonRefAlleleFrequency()));
+            if ( locusdata.hasNonRefAlleleFrequency() )
+                infoFields.put("AF", String.format("%.2f", locusdata.getNonRefAlleleFrequency()));
             Map<String, String> otherFields = locusdata.getFields();
             if ( otherFields != null ) {
                 infoFields.putAll(otherFields);