More pool caller cleanups: ove common duplicated code between Pool and Exact AF calculation models up to super-class to avoid duplication. TMP: Have pool genotypes include the GT field. Mostly because without genotypes we can't get the site-wide AF,AC annotations, but it's unwieldy because it makes the genotype columns very long, TBD final implementation

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

@@ -26,11 +26,14 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
+import java.util.ArrayList;
 import java.util.List;
 
 
@@ -63,6 +66,42 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
         this.verboseWriter = verboseWriter;
     }
 
+    /**
+     * Wrapper class that compares two likelihoods associated with two alleles
+     */
+    protected static final class LikelihoodSum implements Comparable<LikelihoodSum> {
+        public double sum = 0.0;
+        public Allele allele;
+
+        public LikelihoodSum(Allele allele) { this.allele = allele; }
+
+        public int compareTo(LikelihoodSum other) {
+            final double diff = sum - other.sum;
+            return ( diff < 0.0 ) ? 1 : (diff > 0.0 ) ? -1 : 0;
+        }
+    }
+
+    /**
+     * Unpack GenotypesContext into arraylist of doubel values
+     * @param GLs            Input genotype context
+     * @return               ArrayList of doubles corresponding to GL vectors
+     */
+    protected static ArrayList<double[]> getGLs(GenotypesContext GLs) {
+        ArrayList<double[]> genotypeLikelihoods = new ArrayList<double[]>(GLs.size());
+
+        genotypeLikelihoods.add(new double[]{0.0,0.0,0.0}); // dummy
+        for ( Genotype sample : GLs.iterateInSampleNameOrder() ) {
+            if ( sample.hasLikelihoods() ) {
+                double[] gls = sample.getLikelihoods().getAsVector();
+
+                if ( MathUtils.sum(gls) < UnifiedGenotyperEngine.SUM_GL_THRESH_NOCALL )
+                    genotypeLikelihoods.add(gls);
+            }
+        }
+
+        return genotypeLikelihoods;
+    }
+
     /**
      * Must be overridden by concrete subclasses
      * @param vc                                variant context with alleles and genotype likelihoods

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

@@ -56,7 +56,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
             alleles = new ArrayList<Allele>(MAX_ALTERNATE_ALLELES_TO_GENOTYPE + 1);
             alleles.add(vc.getReference());
             alleles.addAll(chooseMostLikelyAlternateAlleles(vc, MAX_ALTERNATE_ALLELES_TO_GENOTYPE));
-            GLs = VariantContextUtils.subsetAlleles(vc, alleles, false);
+            GLs = VariantContextUtils.subsetDiploidAlleles(vc, alleles, false);
         }
 
         linearExactMultiAllelic(GLs, alleles.size() - 1, log10AlleleFrequencyPriors, result);
@@ -64,17 +64,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         return alleles;
     }
 
-    private static final class LikelihoodSum implements Comparable<LikelihoodSum> {
-        public double sum = 0.0;
-        public Allele allele;
-
-        public LikelihoodSum(Allele allele) { this.allele = allele; }
-
-        public int compareTo(LikelihoodSum other) {
-            final double diff = sum - other.sum;
-            return ( diff < 0.0 ) ? 1 : (diff > 0.0 ) ? -1 : 0;
-        }
-    }
 
     private static final int PL_INDEX_OF_HOM_REF = 0;
     private static final List<Allele> chooseMostLikelyAlternateAlleles(VariantContext vc, int numAllelesToChoose) {
@@ -112,22 +101,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         return orderedBestAlleles;
     }
     
-    private static final ArrayList<double[]> getGLs(GenotypesContext GLs) {
-        ArrayList<double[]> genotypeLikelihoods = new ArrayList<double[]>(GLs.size());
-
-        genotypeLikelihoods.add(new double[]{0.0,0.0,0.0}); // dummy
-        for ( Genotype sample : GLs.iterateInSampleNameOrder() ) {
-            if ( sample.hasLikelihoods() ) {
-                double[] gls = sample.getLikelihoods().getAsVector();
-
-                if ( MathUtils.sum(gls) < UnifiedGenotyperEngine.SUM_GL_THRESH_NOCALL )
-                    genotypeLikelihoods.add(gls);
-            }
-        }
-
-        return genotypeLikelihoods;
-    }
-
     // -------------------------------------------------------------------------------------
     //
     // Multi-allelic implementation.
@@ -450,7 +423,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
                                                       final List<Allele> allelesToUse,
                                                       final boolean assignGenotypes,
                                                       final int ploidy) {
-        return VariantContextUtils.subsetAlleles(vc, allelesToUse, assignGenotypes);
+        return VariantContextUtils.subsetDiploidAlleles(vc, allelesToUse, assignGenotypes);
     }
 
     // -------------------------------------------------------------------------------------

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java

@@ -1076,8 +1076,8 @@ public class VariantContextUtils {
      * @param vc            variant context with genotype likelihoods
      * @return genotypes context
      */
-    public static GenotypesContext assignGenotypes(final VariantContext vc) {
+    public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) {
-        return subsetAlleles(vc, vc.getAlleles(), true);
+        return subsetDiploidAlleles(vc, vc.getAlleles(), true);
     }
 
     private static final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
@@ -1091,7 +1091,7 @@ public class VariantContextUtils {
      * @param assignGenotypes    true if we should update the genotypes based on the (subsetted) PLs
      * @return genotypes
      */
-    public static GenotypesContext subsetAlleles(final VariantContext vc,
+    public static GenotypesContext subsetDiploidAlleles(final VariantContext vc,
                                                  final List<Allele> allelesToUse,
                                                  final boolean assignGenotypes) {
 
@@ -1170,7 +1170,7 @@ public class VariantContextUtils {
                 if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL )
                     newGTs.add(new Genotype(g.getSampleName(), NO_CALL_ALLELES, Genotype.NO_LOG10_PERROR, null, attrs, false));
                 else
-                    newGTs.add(assignGenotype(g, newLikelihoods, allelesToUse, attrs));
+                    newGTs.add(assignDiploidGenotype(g, newLikelihoods, allelesToUse, attrs));
             }
         }
 
@@ -1187,7 +1187,7 @@ public class VariantContextUtils {
      *
      * @return genotype
      */
-    private static Genotype assignGenotype(final Genotype originalGT, final double[] newLikelihoods, final List<Allele> allelesToUse, final Map<String, Object> attrs) {
+    private static Genotype assignDiploidGenotype(final Genotype originalGT, final double[] newLikelihoods, final List<Allele> allelesToUse, final Map<String, Object> attrs) {
         final int numNewAltAlleles = allelesToUse.size() - 1;
 
         // find the genotype with maximum likelihoods