Multi-sample calls now have associated meta-data (SLOD, allele freq), which wil

l soon actually be used...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1820 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,47 @@
+package org.broadinstitute.sting.utils.genotype;
+
+
+/**
+ * @author ebanks
+ *         <p/>
+ *         Class GenotypeMetaData
+ *         <p/>
+ *         represents the meta data for a genotype object.
+ */
+public class GenotypeMetaData {
+
+    // the strand score lod
+    private double mSLOD;
+
+    // the allele frequency
+    private double mAlleleFrequency;
+
+    /**
+     * create a basic genotype meta data pbject, given the following fields
+     *
+     * @param strandLOD          the strand score lod
+     * @param alleleFrequency    the allele frequency
+     */
+    public GenotypeMetaData(double strandLOD, double alleleFrequency) {
+        mSLOD = strandLOD;
+        mAlleleFrequency = alleleFrequency;
+    }
+
+    /**
+     * get the strand lod
+     *
+     * @return the strand lod
+     */
+    public double getSLOD() {
+        return mSLOD;
+    }
+
+    /**
+     * get the allele frequency
+     *
+     * @return the allele frequency
+     */
+    public double getAlleleFrequency() {
+        return mAlleleFrequency;
+    }
+}

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

@@ -56,7 +56,7 @@ public interface GenotypeWriter {
      * add a multi-sample call if we support it
      * @param genotypes the list of genotypes, that are backed by sample information
      */
-    public void addMultiSampleCall(List<Genotype> genotypes);
+    public void addMultiSampleCall(List<Genotype> genotypes, GenotypeMetaData metadata);
 
     /**
      * @return true if we support multisample, false otherwise

java/src/org/broadinstitute/sting/utils/genotype/geli/GeliAdapter.java

@@ -161,7 +161,7 @@ public class GeliAdapter implements GenotypeWriter {
      * @param genotypes the list of genotypes, that are backed by sample information
      */
     @Override
-    public void addMultiSampleCall( List<Genotype> genotypes) {
+    public void addMultiSampleCall( List<Genotype> genotypes, GenotypeMetaData metadata) {
         throw new UnsupportedOperationException("Geli binary doesn't support multisample calls");
     }
 

java/src/org/broadinstitute/sting/utils/genotype/geli/GeliTextWriter.java

@@ -124,7 +124,7 @@ public class GeliTextWriter implements GenotypeWriter {
      * @param genotypes the list of genotypes, that are backed by sample information
      */
     @Override
-    public void addMultiSampleCall(List<Genotype> genotypes) {
+    public void addMultiSampleCall(List<Genotype> genotypes, GenotypeMetaData metadata) {
         throw new UnsupportedOperationException("Geli text doesn't support multisample calls");
     }
 

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java

@@ -299,7 +299,7 @@ public class GLFWriter implements GenotypeWriter {
      * @param genotypes the list of genotypes, that are backed by sample information
      */
     @Override
-    public void addMultiSampleCall(List<Genotype> genotypes) {
+    public void addMultiSampleCall(List<Genotype> genotypes, GenotypeMetaData metadata) {
         throw new UnsupportedOperationException("GLF writer doesn't support multisample calls");
     }
 

java/src/org/broadinstitute/sting/utils/genotype/tabular/TabularLFWriter.java

@@ -104,7 +104,7 @@ public class TabularLFWriter implements GenotypeWriter {
      * @param genotypes the list of genotypes, that are backed by sample information
      */
     @Override
-    public void addMultiSampleCall(List<Genotype> genotypes) {
+    public void addMultiSampleCall(List<Genotype> genotypes, GenotypeMetaData metadata) {
         throw new UnsupportedOperationException("Tabular LF doesn't support multisample calls");
     }
 

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

@@ -2,10 +2,7 @@ package org.broadinstitute.sting.utils.genotype.vcf;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.genotype.Genotype;
+import org.broadinstitute.sting.utils.genotype.*;
-import org.broadinstitute.sting.utils.genotype.GenotypeWriter;
-import org.broadinstitute.sting.utils.genotype.ReadBacked;
-import org.broadinstitute.sting.utils.genotype.SampleBacked;
 
 import java.io.File;
 import java.io.OutputStream;
@@ -91,7 +88,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
      */
     @Override
     public void addGenotypeCall(Genotype call) {
-        addMultiSampleCall(Arrays.asList(call));
+        addMultiSampleCall(Arrays.asList(call), null);
     }
 
     /**
@@ -117,7 +114,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
      * @param genotypes the list of genotypes, that are backed by sample information
      */
     @Override
-    public void addMultiSampleCall(List<Genotype> genotypes) {
+    public void addMultiSampleCall(List<Genotype> genotypes, GenotypeMetaData metadata) {
         if (!mInitialized)
             lazyInitialize(genotypes, mFile, mStream);
 
@@ -150,6 +147,8 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
                 params.addAlternateBase(allele);
             }
 
+            // TODO -- use the GenotypeMetaData object if it's not null            
+
             VCFGenotypeRecord record = new VCFGenotypeRecord(((SampleBacked) gtype).getSampleName(),
                                                              alleles,
                                                              VCFGenotypeRecord.PHASE.UNPHASED,