Major refactor/completion of new Pool Caller under UnifiedGenotyper framework. PoolAFCalculationModel implements new math to combine pools - correct, but still O(N^2) and not complete yet for multiallelics. Pool likelihoods are better encapsulated and kept in an internal hashmap from int[] -> double for space efficiency (likelihoods can be big for pool calls when in initial discovery mode with 4 alleles). Maybe need several iterations of optimization to make it runnable at large scale. Still need to correct function chooseMostLikelyAlternateAlleles before full runs can be produced.

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

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
 import java.io.PrintStream;
@@ -72,4 +73,17 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
     protected abstract List<Allele> getLog10PNonRef(final VariantContext vc,
                                                     final double[] log10AlleleFrequencyPriors,
                                                     final AlleleFrequencyCalculationResult result);
+
+    /**
+     * Must be overridden by concrete subclasses
+     * @param vc                                variant context with alleles and genotype likelihoods
+     * @param allelesToUse                      alleles to subset
+     * @param assignGenotypes
+     * @param ploidy
+     * @return GenotypesContext object
+     */
+    protected abstract GenotypesContext subsetAlleles(final VariantContext vc,
+                                                      final List<Allele> allelesToUse,
+                                                      final boolean assignGenotypes,
+                                                      final int ploidy);
 }

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

@@ -446,6 +446,12 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         return coeff;
     }
 
+    public GenotypesContext subsetAlleles(final VariantContext vc,
+                                                      final List<Allele> allelesToUse,
+                                                      final boolean assignGenotypes,
+                                                      final int ploidy) {
+        return VariantContextUtils.subsetAlleles(vc, allelesToUse, assignGenotypes);
+    }
 
     // -------------------------------------------------------------------------------------
     //

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

@@ -357,7 +357,7 @@ public class UnifiedGenotyperEngine {
         }
 
         // create the genotypes
-        final GenotypesContext genotypes = VariantContextUtils.subsetAlleles(vc, myAlleles, true);
+        final GenotypesContext genotypes = afcm.get().subsetAlleles(vc, myAlleles, true,ploidy);
 
         // print out stats if we have a writer
         if ( verboseWriter != null && !limitedContext )

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

@@ -231,7 +231,7 @@ public class GenotypeLikelihoods {
     private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALLELES_THAT_CAN_BE_GENOTYPED); // start with data for 10 alternate alleles
 
     private static GenotypeLikelihoodsAllelePair[] calculatePLcache(final int altAlleles) {
-        final int numLikelihoods = calculateNumLikelihoods(altAlleles);
+        final int numLikelihoods = calculateNumLikelihoods(1+altAlleles, 2);
         final GenotypeLikelihoodsAllelePair[] cache = new GenotypeLikelihoodsAllelePair[numLikelihoods];
 
         // for all possible combinations of 2 alleles
@@ -251,11 +251,22 @@ public class GenotypeLikelihoods {
     }
     
     // how many likelihoods are associated with the given number of alternate alleles?
-    public static int calculateNumLikelihoods(final int numAltAlleles) {
+    public static int calculateNumLikelihoods(final int numAlleles, final int ploidy) {
-        int numLikelihoods = 1;
+
+        if (numAlleles == 1)
+            return 1;
+        else if (ploidy == 1)
+            return numAlleles;
+
+        int acc =0;
+        for (int k=0; k <= ploidy; k++ )
+            acc += calculateNumLikelihoods(numAlleles-1, ploidy-k);
+
+        return acc;
+/*        int numLikelihoods = 1;
         for ( int i = 1; i <= numAltAlleles; i++ )
             numLikelihoods += i + 1;
-        return numLikelihoods;
+        return numLikelihoods;     */
     }
 
     // As per the VCF spec: "the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j.

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

@@ -30,6 +30,7 @@ import org.apache.commons.jexl2.JexlEngine;
 import org.apache.log4j.Logger;
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
 import org.broadinstitute.sting.commandline.Hidden;
+import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
@@ -119,7 +120,7 @@ public class VariantContextUtils {
         builder.attributes(attrs);
     }
 
-    private static String makePrecisionFormatStringFromDenominatorValue(double maxValue) {
+    public static String makePrecisionFormatStringFromDenominatorValue(double maxValue) {
         int precision = 1;
 
         while ( maxValue > 1 ) {
@@ -1116,7 +1117,7 @@ public class VariantContextUtils {
                     altAlleleIndexToUse[i] = true;
             }
 
-            final int numLikelihoods = GenotypeLikelihoods.calculateNumLikelihoods(numOriginalAltAlleles);
+            final int numLikelihoods = GenotypeLikelihoods.calculateNumLikelihoods(numOriginalAltAlleles, UnifiedGenotyperEngine.DEFAULT_PLOIDY);
             for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
                 final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
                 // consider this entry only if both of the alleles are good

public/java/test/org/broadinstitute/sting/BaseTest.java

@@ -84,7 +84,7 @@ public abstract class BaseTest {
     public static final String hg19Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list";
     public static final String hg19Chr20Intervals = intervalsLocation + "whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.chr20.interval_list";
 
-    public static final boolean REQUIRE_NETWORK_CONNECTION = true;
+    public static final boolean REQUIRE_NETWORK_CONNECTION = false;
     public static final String networkTempDir;
     public static final File networkTempDirFile;