Simple cleanup of pool caller code - since usage is much more general than just calling pools, AF calculation models and GL calculation models are renamed from Pool -> GeneralPloidy. Also, don't have users specify special arguments for -glm and -pnrm. Instead, when running UG with sample ploidy != 2, the correct general ploidy modules are automatically detected and loaded. -glm now reverts to old [SNP|INDEL|BOTH] usage

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java

@@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.variantcontext.*;
 import java.io.PrintStream;
 import java.util.*;
 
-public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
+public class GeneralPloidyExactAFCalculationModel extends AlleleFrequencyCalculationModel {
     static final int MAX_LENGTH_FOR_POOL_PL_LOGGING = 10; // if PL vectors longer than this # of elements, don't log them
     final protected UnifiedArgumentCollection UAC;
 
@@ -42,7 +42,7 @@ public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
     private final static double MAX_LOG10_ERROR_TO_STOP_EARLY = 6; // we want the calculation to be accurate to 1 / 10^6
     private final static boolean VERBOSE = false;
 
-    protected PoolAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) {
+    protected GeneralPloidyExactAFCalculationModel(UnifiedArgumentCollection UAC, int N, Logger logger, PrintStream verboseWriter) {
         super(UAC, N, logger, verboseWriter);
         ploidy = UAC.samplePloidy;
         this.UAC = UAC;
@@ -140,7 +140,7 @@ public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
         for ( final double[] likelihoods : GLs ) {
 
             final int PLindexOfBestGL = MathUtils.maxElementIndex(likelihoods);
-            final int[] acCount = PoolGenotypeLikelihoods.getAlleleCountFromPLIndex(1+numOriginalAltAlleles,ploidy,PLindexOfBestGL);
+            final int[] acCount = GeneralPloidyGenotypeLikelihoods.getAlleleCountFromPLIndex(1 + numOriginalAltAlleles, ploidy, PLindexOfBestGL);
             // by convention, first count coming from getAlleleCountFromPLIndex comes from reference allele
             for (int k=1; k < acCount.length;k++) {
                 if (acCount[k] > 0)
@@ -238,7 +238,7 @@ public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
         return newPool;
     }
 
-    // todo - refactor, function almost identical except for log10LofK computation in PoolGenotypeLikelihoods
+    // todo - refactor, function almost identical except for log10LofK computation in GeneralPloidyGenotypeLikelihoods
     /**
      *
      * @param set                       ExactACset holding conformation to be computed
@@ -301,7 +301,7 @@ public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
                 continue;
 
 
-            PoolGenotypeLikelihoods.updateACset(ACcountsClone, ACqueue, indexesToACset);
+            GeneralPloidyGenotypeLikelihoods.updateACset(ACcountsClone, ACqueue, indexesToACset);
         }
 
 
@@ -341,14 +341,14 @@ public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
 
         // Say L1(K) = Pr(D|AC1=K) * choose(m1,K)
         // and L2(K) = Pr(D|AC2=K) * choose(m2,K)
-        PoolGenotypeLikelihoods.SumIterator firstIterator = new PoolGenotypeLikelihoods.SumIterator(numAlleles,ploidy1);
+        GeneralPloidyGenotypeLikelihoods.SumIterator firstIterator = new GeneralPloidyGenotypeLikelihoods.SumIterator(numAlleles,ploidy1);
         final double[] x = originalPool.getLikelihoodsAsVector(true);
         while(firstIterator.hasNext()) {
             x[firstIterator.getLinearIndex()] += MathUtils.log10MultinomialCoefficient(ploidy1,firstIterator.getCurrentVector());
             firstIterator.next();
         }
 
-        PoolGenotypeLikelihoods.SumIterator secondIterator = new PoolGenotypeLikelihoods.SumIterator(numAlleles,ploidy2);
+        GeneralPloidyGenotypeLikelihoods.SumIterator secondIterator = new GeneralPloidyGenotypeLikelihoods.SumIterator(numAlleles,ploidy2);
         final double[] y = yy.clone();
         while(secondIterator.hasNext()) {
             y[secondIterator.getLinearIndex()] += MathUtils.log10MultinomialCoefficient(ploidy2,secondIterator.getCurrentVector());
@@ -357,7 +357,7 @@ public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
 
         // initialize output to -log10(choose(m1+m2,[k1 k2...])
         final int outputDim = GenotypeLikelihoods.numLikelihoods(numAlleles, newPloidy);
-        final PoolGenotypeLikelihoods.SumIterator outputIterator = new PoolGenotypeLikelihoods.SumIterator(numAlleles,newPloidy);
+        final GeneralPloidyGenotypeLikelihoods.SumIterator outputIterator = new GeneralPloidyGenotypeLikelihoods.SumIterator(numAlleles,newPloidy);
 
 
         // Now, result(K) =  logSum_G (L1(G)+L2(K-G)) where G are all possible vectors that sum UP to K
@@ -419,7 +419,7 @@ public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
             double denom =  -MathUtils.log10MultinomialCoefficient(newPloidy, currentCount);
 
             // for current conformation, get all possible ways to break vector K into two components G1 and G2
-            final PoolGenotypeLikelihoods.SumIterator innerIterator = new PoolGenotypeLikelihoods.SumIterator(numAlleles,ploidy2);
+            final GeneralPloidyGenotypeLikelihoods.SumIterator innerIterator = new GeneralPloidyGenotypeLikelihoods.SumIterator(numAlleles,ploidy2);
             set.log10Likelihoods[0] = Double.NEGATIVE_INFINITY;
             while (innerIterator.hasNext()) {
                 // check if breaking current conformation into g1 and g2 is feasible.
@@ -617,7 +617,7 @@ public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
             if ( numOriginalAltAlleles == numNewAltAlleles) {
                 newLikelihoods = originalLikelihoods;
             } else {
-                newLikelihoods = PoolGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(),allelesToUse);
+                newLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(originalLikelihoods, ploidy, vc.getAlleles(), allelesToUse);
 
                 // might need to re-normalize
                 newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
@@ -668,7 +668,7 @@ public class PoolAFCalculationModel extends AlleleFrequencyCalculationModel {
         // find the genotype with maximum likelihoods
         final int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods);
 
-        final int[] mlAlleleCount = PoolGenotypeLikelihoods.getAlleleCountFromPLIndex(allelesToUse.size(), numChromosomes, PLindex);
+        final int[] mlAlleleCount = GeneralPloidyGenotypeLikelihoods.getAlleleCountFromPLIndex(allelesToUse.size(), numChromosomes, PLindex);
         final ArrayList<Double> alleleFreqs = new ArrayList<Double>();
         final ArrayList<Integer> alleleCounts = new ArrayList<Integer>();
 

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java

@@ -37,7 +37,7 @@ import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
 
 import java.util.*;
 
-public abstract class PoolGenotypeLikelihoods {
+public abstract class GeneralPloidyGenotypeLikelihoods {
     protected final int numChromosomes;
     private final static double MAX_LOG10_ERROR_TO_STOP_EARLY = 6; // we want the calculation to be accurate to 1 / 10^6
 
@@ -67,8 +67,8 @@ public abstract class PoolGenotypeLikelihoods {
 
     private static final boolean FAST_GL_COMPUTATION = true;
     // constructor with given logPL elements
-    public PoolGenotypeLikelihoods(final List<Allele> alleles, final double[] logLikelihoods, final int ploidy,
+    public GeneralPloidyGenotypeLikelihoods(final List<Allele> alleles, final double[] logLikelihoods, final int ploidy,
-                                   final HashMap<String, ErrorModel> perLaneErrorModels, final boolean ignoreLaneInformation) {
+                                            final HashMap<String, ErrorModel> perLaneErrorModels, final boolean ignoreLaneInformation) {
         this.alleles = alleles;
         this.nAlleles = alleles.size();
         numChromosomes = ploidy;
@@ -101,7 +101,7 @@ public abstract class PoolGenotypeLikelihoods {
             Arrays.fill(log10Likelihoods, MIN_LIKELIHOOD);
         } else {
             if (logLikelihoods.length != likelihoodDim)
-                throw new ReviewedStingException("BUG: inconsistent parameters when creating PoolGenotypeLikelihoods object");
+                throw new ReviewedStingException("BUG: inconsistent parameters when creating GeneralPloidyGenotypeLikelihoods object");
 
             log10Likelihoods = logLikelihoods; //.clone(); // is clone needed?
         }
@@ -174,7 +174,7 @@ public abstract class PoolGenotypeLikelihoods {
                 final int numAlleles = currentState.length;
                 final int ploidy = restrictSumTo;
 
-                linearIndex = PoolGenotypeLikelihoods.getLinearIndex(stateVector, numAlleles, ploidy);
+                linearIndex = GeneralPloidyGenotypeLikelihoods.getLinearIndex(stateVector, numAlleles, ploidy);
             }
             else
                 throw new ReviewedStingException("BUG: Not supported");
@@ -308,7 +308,7 @@ public abstract class PoolGenotypeLikelihoods {
     public static double[] subsetToAlleles(final double[] oldLikelihoods, final int numChromosomes,
                                                    final List<Allele> originalAlleles, final List<Allele> allelesToSubset) {
 
-        int newPLSize = PoolGenotypeLikelihoods.getNumLikelihoodElements(allelesToSubset.size(), numChromosomes);
+        int newPLSize = GeneralPloidyGenotypeLikelihoods.getNumLikelihoodElements(allelesToSubset.size(), numChromosomes);
         double[] newPLs = new double[newPLSize];
 
 
@@ -357,7 +357,7 @@ public abstract class PoolGenotypeLikelihoods {
                     newCount[idx] =  pVec[permutationKey[idx]];
     
                 // get corresponding index from new count
-                int outputIdx = PoolGenotypeLikelihoods.getLinearIndex(newCount, allelesToSubset.size(), numChromosomes);
+                int outputIdx = GeneralPloidyGenotypeLikelihoods.getLinearIndex(newCount, allelesToSubset.size(), numChromosomes);
                 newPLs[outputIdx] = pl;
                 if (VERBOSE) {
                     System.out.println("Old Key:"+Arrays.toString(pVec));

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java

@@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.util.*;
 
-public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
+public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
 
     //protected Set<String> laneIDs;
     public enum Model {
@@ -52,7 +52,7 @@ public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLi
 
     final protected UnifiedArgumentCollection UAC;
 
-    protected PoolGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
+    protected GeneralPloidyGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
         super(UAC,logger);
         this.UAC = UAC;
 
@@ -137,11 +137,11 @@ public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLi
     protected static class PoolGenotypeData {
 
         public final String name;
-        public final PoolGenotypeLikelihoods GL;
+        public final GeneralPloidyGenotypeLikelihoods GL;
         public final int depth;
         public final List<Allele> alleles;
 
-        public PoolGenotypeData(final String name, final PoolGenotypeLikelihoods GL, final int depth, final List<Allele> alleles) {
+        public PoolGenotypeData(final String name, final GeneralPloidyGenotypeLikelihoods GL, final int depth, final List<Allele> alleles) {
             this.name = name;
             this.GL = GL;
             this.depth = depth;
@@ -236,7 +236,7 @@ public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLi
             ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup();
 
             // create the GenotypeLikelihoods object
-            final PoolGenotypeLikelihoods GL = getPoolGenotypeLikelihoodObject(allAlleles, null, UAC.samplePloidy, perLaneErrorModels, useBAQedPileup, ref, UAC.IGNORE_LANE_INFO);
+            final GeneralPloidyGenotypeLikelihoods GL = getPoolGenotypeLikelihoodObject(allAlleles, null, UAC.samplePloidy, perLaneErrorModels, useBAQedPileup, ref, UAC.IGNORE_LANE_INFO);
             // actually compute likelihoods
             final int nGoodBases = GL.add(pileup, UAC);
             if ( nGoodBases > 0 )
@@ -268,7 +268,7 @@ public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLi
 
         for ( PoolGenotypeData sampleData : GLs ) {
             // extract from multidimensional array
-            final double[] myLikelihoods = PoolGenotypeLikelihoods.subsetToAlleles(sampleData.GL.getLikelihoods(),sampleData.GL.numChromosomes,
+            final double[] myLikelihoods = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(sampleData.GL.getLikelihoods(), sampleData.GL.numChromosomes,
                     allAlleles, alleles);
 
             // normalize in log space so that max element is zero.
@@ -327,7 +327,7 @@ public abstract class PoolGenotypeLikelihoodsCalculationModel extends GenotypeLi
        Abstract methods - must be implemented in derived classes
     */
 
-    protected abstract PoolGenotypeLikelihoods getPoolGenotypeLikelihoodObject(final List<Allele> alleles,
+    protected abstract GeneralPloidyGenotypeLikelihoods getPoolGenotypeLikelihoodObject(final List<Allele> alleles,
                                                                                final double[] logLikelihoods,
                                                                                final int ploidy,
                                                                                final HashMap<String, ErrorModel> perLaneErrorModels,

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java

@@ -18,7 +18,7 @@ import java.util.*;
  * Time: 10:06 AM
  * To change this template use File | Settings | File Templates.
  */
-public class PoolIndelGenotypeLikelihoods extends PoolGenotypeLikelihoods {
+public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotypeLikelihoods {
     final PairHMMIndelErrorModel pairModel;
     final LinkedHashMap<Allele, Haplotype> haplotypeMap;
     final ReferenceContext refContext;
@@ -27,14 +27,14 @@ public class PoolIndelGenotypeLikelihoods extends PoolGenotypeLikelihoods {
 
     final byte refBase;
 
-    public PoolIndelGenotypeLikelihoods(final List<Allele> alleles, 
+    public GeneralPloidyIndelGenotypeLikelihoods(final List<Allele> alleles,
-                                        final double[] logLikelihoods, 
+                                                 final double[] logLikelihoods,
-                                        final int ploidy,
+                                                 final int ploidy,
-                                        final HashMap<String, ErrorModel> perLaneErrorModels, 
+                                                 final HashMap<String, ErrorModel> perLaneErrorModels,
-                                        final boolean ignoreLaneInformation,
+                                                 final boolean ignoreLaneInformation,
-                                        final PairHMMIndelErrorModel pairModel, 
+                                                 final PairHMMIndelErrorModel pairModel,
-                                        final LinkedHashMap<Allele, Haplotype> haplotypeMap,
+                                                 final LinkedHashMap<Allele, Haplotype> haplotypeMap,
-                                        final ReferenceContext referenceContext) {
+                                                 final ReferenceContext referenceContext) {
         super(alleles, logLikelihoods, ploidy, perLaneErrorModels, ignoreLaneInformation);
         this.pairModel = pairModel;
         this.haplotypeMap = haplotypeMap;

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java

@@ -32,13 +32,11 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.util.*;
 
-public class PoolIndelGenotypeLikelihoodsCalculationModel extends PoolGenotypeLikelihoodsCalculationModel {
+public class GeneralPloidyIndelGenotypeLikelihoodsCalculationModel extends GeneralPloidyGenotypeLikelihoodsCalculationModel {
     private static final int MAX_NUM_ALLELES_TO_GENOTYPE = 4;
 
     private PairHMMIndelErrorModel pairModel;
@@ -59,7 +57,7 @@ public class PoolIndelGenotypeLikelihoodsCalculationModel extends PoolGenotypeLi
     }
        */
 
-    protected PoolIndelGenotypeLikelihoodsCalculationModel(final UnifiedArgumentCollection UAC, final Logger logger) {
+    protected GeneralPloidyIndelGenotypeLikelihoodsCalculationModel(final UnifiedArgumentCollection UAC, final Logger logger) {
         super(UAC, logger);
 
 
@@ -69,14 +67,14 @@ public class PoolIndelGenotypeLikelihoodsCalculationModel extends PoolGenotypeLi
     }
 
 
-    protected PoolGenotypeLikelihoods getPoolGenotypeLikelihoodObject(final List<Allele> alleles,
+    protected GeneralPloidyGenotypeLikelihoods getPoolGenotypeLikelihoodObject(final List<Allele> alleles,
                                                                                final double[] logLikelihoods,
                                                                                final int ploidy,
                                                                                final HashMap<String, ErrorModel> perLaneErrorModels,
                                                                                final boolean useBQAedPileup,
                                                                                final ReferenceContext ref,
                                                                                final boolean ignoreLaneInformation){
-        return new PoolIndelGenotypeLikelihoods(alleles, logLikelihoods, ploidy,perLaneErrorModels,ignoreLaneInformation, pairModel, haplotypeMap, ref);
+        return new GeneralPloidyIndelGenotypeLikelihoods(alleles, logLikelihoods, ploidy,perLaneErrorModels,ignoreLaneInformation, pairModel, haplotypeMap, ref);
     }
 
     protected List<Allele> getInitialAllelesToUse(final RefMetaDataTracker tracker,

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java

@@ -23,7 +23,7 @@ import static java.lang.Math.pow;
  * and posteriors given a pile of bases and quality scores
  *
 */
-public class PoolSNPGenotypeLikelihoods extends PoolGenotypeLikelihoods/* implements Cloneable*/ {
+public class GeneralPloidySNPGenotypeLikelihoods extends GeneralPloidyGenotypeLikelihoods/* implements Cloneable*/ {
 
     final List<Allele> myAlleles;
     final int[] alleleIndices;
@@ -42,8 +42,8 @@ public class PoolSNPGenotypeLikelihoods extends PoolGenotypeLikelihoods/* implem
      * @param useBQAedPileup    Use BAQed pileup
      * @param ignoreLaneInformation  If true, lane info is ignored
      */
-    public PoolSNPGenotypeLikelihoods(final List<Allele> alleles, final double[] logLikelihoods, final int ploidy,
+    public GeneralPloidySNPGenotypeLikelihoods(final List<Allele> alleles, final double[] logLikelihoods, final int ploidy,
-                                      final HashMap<String, ErrorModel> perLaneErrorModels, final boolean useBQAedPileup,final boolean ignoreLaneInformation) {
+                                               final HashMap<String, ErrorModel> perLaneErrorModels, final boolean useBQAedPileup, final boolean ignoreLaneInformation) {
         super(alleles, logLikelihoods, ploidy, perLaneErrorModels, ignoreLaneInformation);
         this.useBAQedPileup = useBQAedPileup;
 
@@ -52,7 +52,7 @@ public class PoolSNPGenotypeLikelihoods extends PoolGenotypeLikelihoods/* implem
         Allele refAllele = alleles.get(0);
         //sanity check: by construction, first allele should ALWAYS be the reference alleles
         if (!refAllele.isReference())
-            throw new ReviewedStingException("BUG: First allele in list passed to PoolSNPGenotypeLikelihoods should be reference!");
+            throw new ReviewedStingException("BUG: First allele in list passed to GeneralPloidySNPGenotypeLikelihoods should be reference!");
 
         refByte = refAllele.getBases()[0];  // by construction, first allele in list is always ref!
 

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java

@@ -35,22 +35,22 @@ import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.util.*;
 
-public class PoolSNPGenotypeLikelihoodsCalculationModel extends PoolGenotypeLikelihoodsCalculationModel {
+public class GeneralPloidySNPGenotypeLikelihoodsCalculationModel extends GeneralPloidyGenotypeLikelihoodsCalculationModel {
 
 
-    protected PoolSNPGenotypeLikelihoodsCalculationModel( UnifiedArgumentCollection UAC,  Logger logger) {
+    protected GeneralPloidySNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
         super(UAC, logger);
 
     }
 
-    protected PoolGenotypeLikelihoods getPoolGenotypeLikelihoodObject(final List<Allele> alleles,
+    protected GeneralPloidyGenotypeLikelihoods getPoolGenotypeLikelihoodObject(final List<Allele> alleles,
                                                                                final double[] logLikelihoods,
                                                                                final int ploidy,
                                                                                final HashMap<String, ErrorModel> perLaneErrorModels,
                                                                                final boolean useBQAedPileup,
                                                                                final ReferenceContext ref,
                                                                                final boolean ignoreLaneInformation) {
-        return new PoolSNPGenotypeLikelihoods(alleles, null, UAC.samplePloidy, perLaneErrorModels, useBQAedPileup, UAC.IGNORE_LANE_INFO);
+        return new GeneralPloidySNPGenotypeLikelihoods(alleles, null, UAC.samplePloidy, perLaneErrorModels, useBQAedPileup, UAC.IGNORE_LANE_INFO);
     }
 
     protected List<Allele> getInitialAllelesToUse(final RefMetaDataTracker tracker,

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyAFCalculationModelUnitTest.java

@@ -19,7 +19,7 @@ import java.util.Arrays;
  * Time: 7:44 AM
  * To change this template use File | Settings | File Templates.
  */
-public class PoolAFCalculationModelUnitTest extends BaseTest {
+public class GeneralPloidyAFCalculationModelUnitTest extends BaseTest {
 
     static double[] AA1, AB1, BB1;
     static double[] AA2, AB2, AC2, BB2, BC2, CC2;
@@ -138,10 +138,10 @@ public class PoolAFCalculationModelUnitTest extends BaseTest {
     public void testGLs(GetGLsTest cfg) {
 
         final AlleleFrequencyCalculationResult result = new AlleleFrequencyCalculationResult(cfg.numAltAlleles);
-        final int len = PoolGenotypeLikelihoods.getNumLikelihoodElements(1+cfg.numAltAlleles,cfg.ploidy*cfg.GLs.size());
+        final int len = GeneralPloidyGenotypeLikelihoods.getNumLikelihoodElements(1 + cfg.numAltAlleles, cfg.ploidy * cfg.GLs.size());
         double[] priors = new double[len];  // flat priors
 
-        PoolAFCalculationModel.combineSinglePools(cfg.GLs, 1+cfg.numAltAlleles, cfg.ploidy, priors, result);
+        GeneralPloidyExactAFCalculationModel.combineSinglePools(cfg.GLs, 1 + cfg.numAltAlleles, cfg.ploidy, priors, result);
         int nameIndex = 1;
         for ( int allele = 0; allele < cfg.numAltAlleles; allele++, nameIndex+=2 ) {
             int expectedAlleleCount = Integer.valueOf(cfg.name.substring(nameIndex, nameIndex+1));

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java

@@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 import net.sf.samtools.SAMUtils;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.MathUtils;
@@ -42,7 +41,7 @@ import java.io.PrintStream;
 import java.util.*;
 
 
-public class PoolGenotypeLikelihoodsUnitTest {
+public class GeneralPloidyGenotypeLikelihoodsUnitTest {
 
     final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
     final Logger logger = Logger.getLogger(Walker.class);
@@ -61,7 +60,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
     public void testStoringLikelihoodElements() {
 
 
-        // basic test storing a given PL vector in a PoolGenotypeLikelihoods object and then retrieving it back
+        // basic test storing a given PL vector in a GeneralPloidyGenotypeLikelihoods object and then retrieving it back
 
         int ploidy = 20;
         int numAlleles = 4;
@@ -79,7 +78,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
         for (int k=0; k < gls.length; k++)
             gls[k]= (double)k;
 
-        PoolGenotypeLikelihoods gl = new PoolSNPGenotypeLikelihoods(alleles, gls,ploidy, null, false,true);
+        GeneralPloidyGenotypeLikelihoods gl = new GeneralPloidySNPGenotypeLikelihoods(alleles, gls,ploidy, null, false,true);
         double[] glnew = gl.getLikelihoods();
 
         Assert.assertEquals(gls, glnew);
@@ -91,7 +90,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
 
         for (int ploidy = 2; ploidy < 10; ploidy++) {
             for (int nAlleles = 2; nAlleles < 10; nAlleles++)
-                Assert.assertEquals(PoolGenotypeLikelihoods.getNumLikelihoodElements(nAlleles,ploidy),
+                Assert.assertEquals(GeneralPloidyGenotypeLikelihoods.getNumLikelihoodElements(nAlleles, ploidy),
                         GenotypeLikelihoods.numLikelihoods(nAlleles, ploidy));
         }
 
@@ -103,7 +102,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
         // create iterator, compare linear index given by iterator with closed form function
         int numAlleles = 4;
         int ploidy = 2;
-        PoolGenotypeLikelihoods.SumIterator iterator = new PoolGenotypeLikelihoods.SumIterator(numAlleles, ploidy);
+        GeneralPloidyGenotypeLikelihoods.SumIterator iterator = new GeneralPloidyGenotypeLikelihoods.SumIterator(numAlleles, ploidy);
 
         while(iterator.hasNext()) {
             System.out.format("\n%d:",iterator.getLinearIndex());
@@ -112,7 +111,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
                 System.out.format("%d ",aa);
 
 
-            int computedIdx = PoolGenotypeLikelihoods.getLinearIndex(a, numAlleles, ploidy);
+            int computedIdx = GeneralPloidyGenotypeLikelihoods.getLinearIndex(a, numAlleles, ploidy);
             System.out.format("Computed idx = %d\n",computedIdx);
             iterator.next();
         }
@@ -141,7 +140,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
         allelesToSubset.add(Allele.create("A",false));
         allelesToSubset.add(Allele.create("C",false));
 
-        double[] newGLs = PoolGenotypeLikelihoods.subsetToAlleles(oldLikelihoods, ploidy,
+        double[] newGLs = GeneralPloidyGenotypeLikelihoods.subsetToAlleles(oldLikelihoods, ploidy,
                 originalAlleles, allelesToSubset);
 
 
@@ -171,7 +170,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
     @Test
     public void testIndexIterator() {
         int[] seed = new int[]{1,2,3,4};
-        PoolGenotypeLikelihoods.SumIterator iterator = runIterator(seed,-1);
+        GeneralPloidyGenotypeLikelihoods.SumIterator iterator = runIterator(seed,-1);
         // Assert.assertTrue(compareIntArrays(iterator.getCurrentVector(), seed));
         Assert.assertEquals(iterator.getLinearIndex(),prod(seed)-1);
 
@@ -229,12 +228,12 @@ public class PoolGenotypeLikelihoodsUnitTest {
 
     }
 
-    private PoolGenotypeLikelihoods.SumIterator runIterator(int[] seed, int restrictSumTo) {
+    private GeneralPloidyGenotypeLikelihoods.SumIterator runIterator(int[] seed, int restrictSumTo) {
-        PoolGenotypeLikelihoods.SumIterator iterator = new PoolGenotypeLikelihoods.SumIterator(seed, restrictSumTo);
+        GeneralPloidyGenotypeLikelihoods.SumIterator iterator = new GeneralPloidyGenotypeLikelihoods.SumIterator(seed, restrictSumTo);
 
         while(iterator.hasNext()) {
             int[] a =  iterator.getCurrentVector();
-            int idx = PoolGenotypeLikelihoods.getLinearIndex(a, a.length, restrictSumTo);
+            int idx = GeneralPloidyGenotypeLikelihoods.getLinearIndex(a, a.length, restrictSumTo);
             if (VERBOSE)   {
                 System.out.format("%d:",iterator.getLinearIndex());
                 for (int i=0; i < seed.length; i++)
@@ -454,7 +453,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
 
                     // get now likelihoods for this
 
-                    final PoolSNPGenotypeLikelihoods GL = new PoolSNPGenotypeLikelihoods(allAlleles, null, nSamplesPerPool*2, noiselessErrorModels, false, true);
+                    final GeneralPloidySNPGenotypeLikelihoods GL = new GeneralPloidySNPGenotypeLikelihoods(allAlleles, null, nSamplesPerPool*2, noiselessErrorModels, false, true);
                     final int nGoodBases = GL.add(alignmentContextMap.get("sample0000").getBasePileup(), true, false, UAC.MIN_BASE_QUALTY_SCORE);
                     if (VERBOSE) {
                         System.out.format("Depth:%d, AC:%d, altDepth:%d, samplesPerPool:%d\nGLs:", depth,ac,altDepth, nSamplesPerPool);
@@ -483,7 +482,7 @@ public class PoolGenotypeLikelihoodsUnitTest {
 
                             // get now likelihoods for this
 
-                            final PoolSNPGenotypeLikelihoods noisyGL = new PoolSNPGenotypeLikelihoods(allAlleles, null, nSamplesPerPool*2, noisyErrorModels, false,true);
+                            final GeneralPloidySNPGenotypeLikelihoods noisyGL = new GeneralPloidySNPGenotypeLikelihoods(allAlleles, null, nSamplesPerPool*2, noisyErrorModels, false,true);
                             noisyGL.add(noisyAlignmentContextMap.get("sample0000").getBasePileup(), true, false, UAC.MIN_BASE_QUALTY_SCORE);
                             mlPair = noisyGL.getMostLikelyACCount();
 

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java

@@ -12,7 +12,7 @@ import org.testng.annotations.Test;
  * Time: 11:28 AM
  * To change this template use File | Settings | File Templates.
  */
-public class PoolCallerIntegrationTest extends WalkerTest {
+public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
     final static String REF = b37KGReference;
     final String CEUTRIO_BAM = "/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37.list";
     final String LSV_BAM = validationDataLocation +"93pools_NA12878_ref_chr20_40m_41m.bam";
@@ -24,21 +24,21 @@ public class PoolCallerIntegrationTest extends WalkerTest {
     final String NA12878_WG_CALLS = comparisonDataLocation + "Unvalidated/NA12878/CEUTrio.HiSeq.WGS.b37_decoy.recal.ts_95.snp_indel_combined.vcf";
     final String LSV_ALLELES = validationDataLocation + "ALL.chr20_40m_41m.largeScaleValidationSites.vcf";
     private void PC_MT_Test(String bam, String args, String name, String md5) {
-        final String base = String.format("-T UnifiedGenotyper -dcov 10000 -R %s -I %s -L %s --reference_sample_calls %s -refsample %s -glm POOLSNP -ignoreLane -pnrm POOL",
+        final String base = String.format("-T UnifiedGenotyper -dcov 10000 -R %s -I %s -L %s --reference_sample_calls %s -refsample %s -ignoreLane ",
                 REF, bam, MTINTERVALS, REFSAMPLE_MT_CALLS, REFSAMPLE_NAME) + " --no_cmdline_in_header -o %s";
         final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testPoolCaller:"+name+" args=" + args, spec);
     }
 
     private void PC_LSV_Test(String args, String name, String model, String md5) {
-        final String base = String.format("-T UnifiedGenotyper -dcov 10000 -R %s -I %s -L %s --reference_sample_calls %s -refsample %s -glm %s -ignoreLane -pnrm POOL",
+        final String base = String.format("-T UnifiedGenotyper -dcov 10000 -R %s -I %s -L %s --reference_sample_calls %s -refsample %s -glm %s -ignoreLane ",
                 REF, LSV_BAM, LSVINTERVALS, NA12878_WG_CALLS, REFSAMPLE_NAME, model) + " --no_cmdline_in_header -o %s";
         final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testPoolCaller:"+name+" args=" + args, spec);
     }
 
     private void PC_LSV_Test_NoRef(String args, String name, String model, String md5) {
-        final String base = String.format("-T UnifiedGenotyper -dcov 10000 -R %s -I %s -L %s -glm %s -ignoreLane -pnrm POOL",
+        final String base = String.format("-T UnifiedGenotyper -dcov 10000 -R %s -I %s -L %s -glm %s -ignoreLane",
                 REF, LSV_BAM, LSVINTERVALS, model) + " --no_cmdline_in_header -o %s";
         final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
         executeTest("testPoolCaller:"+name+" args=" + args, spec);
@@ -46,22 +46,22 @@ public class PoolCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testBOTH_GGA_Pools() {
-        PC_LSV_Test(String.format(" -maxAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","POOLBOTH","d76e3b910259da819f1e1b2adc68ba8d");
+        PC_LSV_Test(String.format(" -maxAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","d76e3b910259da819f1e1b2adc68ba8d");
     }
 
     @Test
     public void testINDEL_GGA_Pools() {
-        PC_LSV_Test(String.format(" -maxAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","POOLINDEL","ffadcdaee613dab975197bed0fc78da3");
+        PC_LSV_Test(String.format(" -maxAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","ffadcdaee613dab975197bed0fc78da3");
     }
 
     @Test
     public void testINDEL_maxAlleles2_ploidy3_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","POOLINDEL","96087fe9240e3656cc2a4e0ff0174d5b");
+        PC_LSV_Test_NoRef(" -maxAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","96087fe9240e3656cc2a4e0ff0174d5b");
     }
 
     @Test
     public void testINDEL_maxAlleles2_ploidy1_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","POOLINDEL","6fdae7093831ecfc82a06dd707d62fe9");
+        PC_LSV_Test_NoRef(" -maxAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","6fdae7093831ecfc82a06dd707d62fe9");
     }
 
     @Test

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

@@ -46,8 +46,7 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
 
     public enum Model {
         /** The default model with the best performance in all cases */
-        EXACT,
+        EXACT
-        POOL
     }
 
     protected int N;

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

@@ -59,10 +59,9 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
     public enum Model {
         SNP,
         INDEL,
-        BOTH,
+        GeneralPloidySNP,
-        POOLSNP,
+        GeneralPloidyINDEL,
-        POOLINDEL,
+        BOTH
-        POOLBOTH
     }
 
     public enum GENOTYPING_MODE {

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

@@ -241,7 +241,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
         } else {
             // in full mode: check for consistency in ploidy/pool calling arguments
             // check for correct calculation models
-            if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) {
+/*            if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) {
                 // polyploidy requires POOL GL and AF calculation models to be specified right now
                 if (UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLSNP && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLINDEL
                         && UAC.GLmodel != GenotypeLikelihoodsCalculationModel.Model.POOLBOTH)   {
@@ -252,6 +252,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
                     throw new UserException("Incorrect AF Calculation model. Only POOL model supported if sample ploidy != 2");
 
             }
+  */
             // get all of the unique sample names
             if (UAC.TREAT_ALL_READS_AS_SINGLE_POOL) {
                 samples.clear();

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

@@ -50,6 +50,7 @@ import java.util.*;
 
 public class UnifiedGenotyperEngine {
     public static final String LOW_QUAL_FILTER_NAME = "LowQual";
+    private static final String GPSTRING = "GeneralPloidy";
 
     public static final String NUMBER_OF_DISCOVERED_ALLELES_KEY = "NDA";
 
@@ -273,7 +274,7 @@ public class UnifiedGenotyperEngine {
             glcm.set(getGenotypeLikelihoodsCalculationObject(logger, UAC));
         }
 
-        return glcm.get().get(model.name()).getLikelihoods(tracker, refContext, stratifiedContexts, type, alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser);
+        return glcm.get().get(model.name().toUpperCase()).getLikelihoods(tracker, refContext, stratifiedContexts, type, alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser);
     }
 
     private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, AlignmentContext rawContext) {
@@ -640,6 +641,9 @@ public class UnifiedGenotyperEngine {
         if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") )
             modelPrefix = UAC.GLmodel.name().toUpperCase().replaceAll("BOTH","");
 
+        if (!UAC.GLmodel.name().contains(GPSTRING) && UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY)
+            modelPrefix = GPSTRING + modelPrefix;
+
         // if we're genotyping given alleles and we have a requested SNP at this position, do SNP
         if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ) {
             final VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
@@ -648,17 +652,13 @@ public class UnifiedGenotyperEngine {
 
             if ( vcInput.isSNP() )  {
                 // ignore SNPs if the user chose INDEL mode only
-                if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") )
+                if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("SNP") )
                     models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"SNP"));
-                else if ( UAC.GLmodel.name().toUpperCase().contains("SNP") )
+             }
-                    models.add(UAC.GLmodel);
-            }
             else if ( vcInput.isIndel() || vcInput.isMixed() ) {
                 // ignore INDELs if the user chose SNP mode only
-                if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") )
+                if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") || UAC.GLmodel.name().toUpperCase().contains("INDEL") )
                     models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"INDEL"));
-                else if (UAC.GLmodel.name().toUpperCase().contains("INDEL"))
-                    models.add(UAC.GLmodel);
             }
             // No support for other types yet
         }
@@ -668,7 +668,7 @@ public class UnifiedGenotyperEngine {
                 models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+"INDEL"));
             }
             else {
-                models.add(UAC.GLmodel);
+                models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix+UAC.GLmodel.name().toUpperCase()));
             }
         }
 
@@ -730,12 +730,19 @@ public class UnifiedGenotyperEngine {
     }
 
     private static AlleleFrequencyCalculationModel getAlleleFrequencyCalculationObject(int N, Logger logger, PrintStream verboseWriter, UnifiedArgumentCollection UAC) {
+
         List<Class<? extends AlleleFrequencyCalculationModel>> afClasses = new PluginManager<AlleleFrequencyCalculationModel>(AlleleFrequencyCalculationModel.class).getPlugins();
 
+        // user-specified name
+        String afModelName = UAC.AFmodel.name();
+
+        if (!afModelName.contains(GPSTRING) && UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY)
+            afModelName = GPSTRING + afModelName;
+
         for (int i = 0; i < afClasses.size(); i++) {
             Class<? extends AlleleFrequencyCalculationModel> afClass = afClasses.get(i);
             String key = afClass.getSimpleName().replace("AFCalculationModel","").toUpperCase();
-            if (UAC.AFmodel.name().equalsIgnoreCase(key)) {
+            if (afModelName.equalsIgnoreCase(key)) {
                 try {
                     Object args[] = new Object[]{UAC,N,logger,verboseWriter};
                     Constructor c = afClass.getDeclaredConstructor(UnifiedArgumentCollection.class, int.class, Logger.class, PrintStream.class);