Pull the genotype (and genotype quality) calculation out of the VCF code and into the Genotyper.

[Also, enable Mark's new UG arguments]



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2355 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -31,7 +31,6 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
         // use flat priors for GLs
         DiploidGenotypePriors priors = new DiploidGenotypePriors();
 
-        int index = 0;
         for ( String sample : contexts.keySet() ) {
             StratifiedAlignmentContext context = contexts.get(sample);
             ReadBackedPileup pileup = context.getContext(contextType).getPileup();
@@ -47,12 +46,11 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
             DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
             for ( char alt : BaseUtils.BASES ) {
                 if ( alt != ref ) {
-                    DiploidGenotype hetGenotype = ref < alt ? DiploidGenotype.valueOf(String.valueOf(ref) + String.valueOf(alt)) : DiploidGenotype.valueOf(String.valueOf(alt) + String.valueOf(ref));
+                    DiploidGenotype hetGenotype = DiploidGenotype.unorderedValueOf(ref, alt);
                     DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
-                    AFMatrixMap.get(alt).setLikelihoods(posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()], index);
+                    AFMatrixMap.get(alt).setLikelihoods(posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()], sample);
                 }
             }
-            index++;
         }
     }
 
@@ -74,14 +72,31 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
         }
     }
 
-    protected List<Genotype> makeGenotypeCalls(char ref, char alt, Map<String, StratifiedAlignmentContext> contexts, GenomeLoc loc) {
+    protected List<Genotype> makeGenotypeCalls(char ref, char alt, int frequency, Map<String, StratifiedAlignmentContext> contexts, GenomeLoc loc) {
         ArrayList<Genotype> calls = new ArrayList<Genotype>();
 
+        // set up some variables we'll need in the loop
+        AlleleFrequencyMatrix matrix = AFMatrixMap.get(alt);
+        DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
+        DiploidGenotype hetGenotype = DiploidGenotype.unorderedValueOf(ref, alt);
+        DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
+
         for ( String sample : GLs.keySet() ) {
 
             // create the call
             GenotypeCall call = GenotypeWriterFactory.createSupportedGenotypeCall(OUTPUT_FORMAT, ref, loc);
 
+            // set the genotype and confidence
+            Pair<Integer, Double> AFbasedGenotype = matrix.getGenotype(frequency, sample);
+            call.setNegLog10PError(AFbasedGenotype.second);
+            if ( AFbasedGenotype.first == GenotypeType.REF.ordinal() )
+                call.setGenotype(refGenotype);
+            else if ( AFbasedGenotype.first == GenotypeType.HET.ordinal() )
+                call.setGenotype(hetGenotype);
+            else // ( AFbasedGenotype.first == GenotypeType.HOM.ordinal() )
+                call.setGenotype(homGenotype);
+
+
             if ( call instanceof ReadBacked ) {
                 ReadBackedPileup pileup = contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.MQ0FREE).getPileup();
                 ((ReadBacked)call).setPileup(pileup);
@@ -105,12 +120,17 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
         return calls;
     }
 
+
     protected class AlleleFrequencyMatrix {
 
-        private double[][] matrix;
+        private double[][] matrix;    // allele frequency matrix
-        private int[] indexes;
+        private int[] indexes;        // matrix to maintain which genotype is active
-        private int N;
+        private int N;                // total frequencies
-        private int frequency;
+        private int frequency;        // current frequency
+
+        // data structures necessary to maintain a list of the best genotypes and their scores
+        private ArrayList<String> samples = new ArrayList<String>();
+        private HashMap<Integer, HashMap<String, Pair<Integer, Double>>> samplesToGenotypesPerAF = new HashMap<Integer, HashMap<String, Pair<Integer, Double>>>();
 
         public AlleleFrequencyMatrix(int N) {
             this.N = N;
@@ -121,7 +141,9 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
                 indexes[i] = 0;
         }
 
-        public void setLikelihoods(double AA, double AB, double BB, int index) {
+        public void setLikelihoods(double AA, double AB, double BB, String sample) {
+            int index = samples.size();
+            samples.add(sample);
             matrix[index][GenotypeType.REF.ordinal()] = AA;
             matrix[index][GenotypeType.HET.ordinal()] = AB;
             matrix[index][GenotypeType.HOM.ordinal()] = BB;
@@ -169,17 +191,48 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
             for (int i = 0; i < N; i++)
                 likelihoods += matrix[i][indexes[i]];
 
-            //verboseWriter.write(frequency + "\n");
+            /*
-            //for (int i = 0; i < N; i++) {
+            System.out.println(frequency);
-            //    for (int j=0; j < 3; j++) {
+            for (int i = 0; i < N; i++) {
-            //        verboseWriter.write(String.valueOf(matrix[i][j]));
+                for (int j=0; j < 3; j++) {
-            //        verboseWriter.write(indexes[i] == j ? "* " : " ");
+                    System.out.print(String.valueOf(matrix[i][j]));
-            //    }
+                    System.out.print(indexes[i] == j ? "* " : " ");
-            //    verboseWriter.write("\n");
+                }
-            //}
+                System.out.println();
-            //verboseWriter.write(likelihoods + "\n\n");
+            }
+            System.out.println(likelihoods);
+            System.out.println();
+            */
+
+            recordGenotypes();
 
             return likelihoods;
         }
+
+        public Pair<Integer, Double> getGenotype(int frequency, String sample) {
+            return samplesToGenotypesPerAF.get(frequency).get(sample);
+        }
+
+        private void recordGenotypes() {
+            HashMap<String, Pair<Integer, Double>> samplesToGenotypes = new HashMap<String, Pair<Integer, Double>>();
+
+            int index = 0;
+            for ( String sample : samples ) {
+                int genotype = indexes[index];
+
+                double score;
+                if ( genotype == GenotypeType.REF.ordinal() )
+                    score = matrix[index][GenotypeType.REF.ordinal()] - Math.max(matrix[index][GenotypeType.HET.ordinal()], matrix[index][GenotypeType.HOM.ordinal()]);
+                else if ( genotype == GenotypeType.HET.ordinal() )
+                    score = matrix[index][GenotypeType.HET.ordinal()] - Math.max(matrix[index][GenotypeType.REF.ordinal()], matrix[index][GenotypeType.HOM.ordinal()]);
+                else // ( genotype == GenotypeType.HOM.ordinal() )
+                    score = matrix[index][GenotypeType.HOM.ordinal()] - Math.max(matrix[index][GenotypeType.REF.ordinal()], matrix[index][GenotypeType.HET.ordinal()]);
+
+                samplesToGenotypes.put(sample, new Pair<Integer, Double>(genotype, Math.abs(score)));
+                index++;
+            }
+
+            samplesToGenotypesPerAF.put(frequency, samplesToGenotypes);
+        }
     }
 }

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

@@ -96,6 +96,14 @@ public abstract class EMGenotypeCalculationModel extends GenotypeCalculationMode
             AlignmentContext context = contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.MQ0FREE);
             GenotypeCall call = GenotypeWriterFactory.createSupportedGenotypeCall(OUTPUT_FORMAT, ref, context.getLocation());
 
+            // set the genotype and confidence
+            double[] posteriors = GLs.get(sample).getPosteriors();
+            Integer sorted[] = Utils.SortPermutation(posteriors);
+            DiploidGenotype bestGenotype = DiploidGenotype.values()[sorted[DiploidGenotype.values().length - 1]];
+            DiploidGenotype nextGenotype = DiploidGenotype.values()[sorted[DiploidGenotype.values().length - 2]];
+            call.setNegLog10PError(posteriors[bestGenotype.ordinal()] - posteriors[nextGenotype.ordinal()]);
+            call.setGenotype(bestGenotype);
+
             if ( call instanceof ReadBacked ) {
                 ReadBackedPileup pileup = contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.MQ0FREE).getPileup();
                 ((ReadBacked)call).setPileup(pileup);
@@ -107,7 +115,7 @@ public abstract class EMGenotypeCalculationModel extends GenotypeCalculationMode
                 ((LikelihoodsBacked)call).setLikelihoods(GLs.get(sample).getLikelihoods());
             }
             if ( call instanceof PosteriorsBacked ) {
-                ((PosteriorsBacked)call).setPosteriors(GLs.get(sample).getPosteriors());
+                ((PosteriorsBacked)call).setPosteriors(posteriors);
             }
 
             calls.add(call);

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

@@ -299,7 +299,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
         verboseWriter.println();
     }
 
-    protected List<Genotype> makeGenotypeCalls(char ref, char alt, Map<String, StratifiedAlignmentContext> contexts, GenomeLoc loc) {
+    protected List<Genotype> makeGenotypeCalls(char ref, char alt, int frequency, Map<String, StratifiedAlignmentContext> contexts, GenomeLoc loc) {
         // by default, we return no genotypes
         return new ArrayList<Genotype>();
     }    
@@ -329,7 +329,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
             return new Pair<VariationCall, List<Genotype>>(null, null);
 
         // populate the sample-specific data
-        List<Genotype> calls = makeGenotypeCalls(ref, bestAlternateAllele, contexts, loc);
+        List<Genotype> calls = makeGenotypeCalls(ref, bestAlternateAllele, bestAFguess, contexts, loc);
 
         // next, the general locus data
         // *** note that calculating strand bias involves overwriting data structures, so we do that last

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

@@ -43,9 +43,9 @@ public class PointEstimateGenotypeCalculationModel extends EMGenotypeCalculation
             Pair<ReadBackedPileup, GenotypeLikelihoods> discoveryGL = getSingleSampleLikelihoods(sampleContext, priors, StratifiedAlignmentContext.StratifiedContextType.MQ0FREE);
 
             // find the index of the best genotype
-            double[] posteriors = discoveryGL.second.getNormalizedPosteriors();
+            double[] normPosteriors = discoveryGL.second.getNormalizedPosteriors();
-            Integer sortedPosteriors[] = Utils.SortPermutation(posteriors);
+            Integer sortedNormPosteriors[] = Utils.SortPermutation(normPosteriors);
-            int bestIndex = sortedPosteriors[sortedPosteriors.length - 1];
+            int bestIndex = sortedNormPosteriors[sortedNormPosteriors.length - 1];
 
             // flag to determine if ref is the best call (not necessary in genotype mode)
             boolean bestIsRef = false;
@@ -53,11 +53,11 @@ public class PointEstimateGenotypeCalculationModel extends EMGenotypeCalculation
             // calculate the phred-scaled confidence score
             double phredScaledConfidence;
             if ( GENOTYPE_MODE ) {
-                phredScaledConfidence = QualityUtils.phredScaleErrorRate(1.0 - posteriors[bestIndex]);
+                phredScaledConfidence = QualityUtils.phredScaleErrorRate(1.0 - normPosteriors[bestIndex]);
             } else {
                 int refIndex = DiploidGenotype.createHomGenotype(ref).ordinal();
                 bestIsRef = (refIndex == bestIndex);
-                double pError = (bestIsRef ? 1.0 - posteriors[refIndex] : posteriors[refIndex]);
+                double pError = (bestIsRef ? 1.0 - normPosteriors[refIndex] : normPosteriors[refIndex]);
                 phredScaledConfidence = QualityUtils.phredScaleErrorRate(pError);
             }
 
@@ -68,6 +68,14 @@ public class PointEstimateGenotypeCalculationModel extends EMGenotypeCalculation
             // we can now create the genotype call object
             GenotypeCall call = GenotypeWriterFactory.createSupportedGenotypeCall(OUTPUT_FORMAT, ref, loc);
 
+            // set the genotype and confidence
+            double[] posteriors = discoveryGL.second.getPosteriors();
+            Integer sorted[] = Utils.SortPermutation(posteriors);
+            DiploidGenotype bestGenotype = DiploidGenotype.values()[sorted[DiploidGenotype.values().length - 1]];
+            DiploidGenotype nextGenotype = DiploidGenotype.values()[sorted[DiploidGenotype.values().length - 2]];
+            call.setNegLog10PError(posteriors[bestGenotype.ordinal()] - posteriors[nextGenotype.ordinal()]);
+            call.setGenotype(bestGenotype);
+
             if ( call instanceof ReadBacked ) {
                 ((ReadBacked)call).setPileup(discoveryGL.first);
             }
@@ -78,7 +86,7 @@ public class PointEstimateGenotypeCalculationModel extends EMGenotypeCalculation
                 ((LikelihoodsBacked)call).setLikelihoods(discoveryGL.second.getLikelihoods());
             }
             if ( call instanceof PosteriorsBacked ) {
-                ((PosteriorsBacked)call).setPosteriors(discoveryGL.second.getPosteriors());
+                ((PosteriorsBacked)call).setPosteriors(posteriors);
             }
 
             VariationCall locusdata = GenotypeWriterFactory.createSupportedCall(OUTPUT_FORMAT, ref, loc, bestIsRef ? Variation.VARIANT_TYPE.REFERENCE : Variation.VARIANT_TYPE.SNP);

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

@@ -88,10 +88,9 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "min_allele_frequency", shortName = "min_freq", doc = "The minimum possible allele frequency in a population (advanced)", required = false)
     public double MINIMUM_ALLELE_FREQUENCY = 1e-8;
 
-    // Mark's filtering arguments
+    @Argument(fullName = "minBaseQualityScore", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
-    //@Argument(fullName = "minBaseQualityScore", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
     public Integer MIN_BASE_QUALTY_SCORE = -1;
 
-    //@Argument(fullName = "minMappingQualityScore", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
+    @Argument(fullName = "minMappingQualityScore", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for calling", required = false)
     public Integer MIN_MAPPING_QUALTY_SCORE = -1;
 }

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

@@ -8,7 +8,7 @@ package org.broadinstitute.sting.utils.genotype;
  *         <p/>
  *         A genotype that can have only one of 3 genotypes AA,AB,BB
  */
-public abstract class AlleleConstrainedGenotype implements Genotype, PosteriorsBacked {
+public abstract class AlleleConstrainedGenotype implements Genotype {
 
     protected final static char NO_CONSTRAINT = 'N';
 
@@ -36,6 +36,7 @@ public abstract class AlleleConstrainedGenotype implements Genotype, PosteriorsB
     }
 
     /**
+     * 
      * @return returns the best genotype
      */
     protected abstract DiploidGenotype getBestGenotype();

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

@@ -44,13 +44,7 @@ public enum DiploidGenotype {
     }
 
     public boolean isHet() {
-        switch (this) {
+        return base1 != base2;
-            case AA:
-            case CC:
-            case GG:
-            case TT: return false;
-            default: return true;
-        }
     }
 
     /**
@@ -71,14 +65,16 @@ public enum DiploidGenotype {
 
     /**
      * get the genotype, given a string of 2 chars which may not necessarily be ordered correctly
-     * @param genotype the string representation
+     * @param base1 base1
+     * @param base2 base2
      * @return the diploid genotype
      */
-    public static DiploidGenotype unorderedValueOf(String genotype) {
+    public static DiploidGenotype unorderedValueOf(char base1, char base2) {
-        if ( genotype == null || genotype.length() != 2 )
+        if ( base1 > base2 ) {
-            throw new IllegalArgumentException("Diploid genotypes are represented by 2 characters");
+            char temp = base1;
-        if ( genotype.charAt(0) > genotype.charAt(1) )
+            base1 = base2;
-            genotype = String.format("%c%c", genotype.charAt(1), genotype.charAt(0));
+            base2 = temp;
-        return valueOf(genotype);
+        }
+        return valueOf(String.format("%c%c", base1, base2));
     }
 }

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

@@ -12,8 +12,20 @@ public interface GenotypeCall extends Genotype {
 
     /**
      *
-     * @param   variation    the Variation object associated with this genotype
+     * @param   variation   the Variation object associated with this genotype
      */
     public void setVariation(Variation variation);
 
+    /**
+     *
+     * @param   genotype    the genotype
+     */
+    public void setGenotype(DiploidGenotype genotype);
+
+    /**
+     *
+     * @param   value       -log10PEror
+     */
+    public void setNegLog10PError(double value);
+
 }

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

@@ -4,8 +4,8 @@ package org.broadinstitute.sting.utils.genotype;
  * @author aaron
  * Interface PosteriorsBacked
  *
- * this interface indicates that the genotype is
+ * This interface indicates that the genotype is backed up by *diploid* genotype posterior information.
- * backed up by genotype posterior information.
+ * The posteriors array is expected to have 10 entries (one for each of the possible diploid genotypes).
  */
 public interface PosteriorsBacked {
 

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

@@ -82,6 +82,14 @@ public class GeliGenotypeCall extends AlleleConstrainedGenotype implements Genot
         this.mVariation = variation;
     }
 
+    public void setGenotype(DiploidGenotype genotype) {
+        ; // do nothing: geli uses diploid posteriors to calculate the genotype
+    }
+
+    public void setNegLog10PError(double value) {
+        ; // do nothing: geli uses diploid posteriors to calculate the P(error)
+    }
+
     @Override
     public boolean equals(Object other) {
         lazyEval();

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

@@ -65,6 +65,10 @@ public class GLFGenotypeCall implements GenotypeCall, ReadBacked, LikelihoodsBac
         mGenotype = genotype;
     }
 
+    public void setGenotype(DiploidGenotype genotype) {
+        setGenotype(genotype.toString());
+    }
+
     @Override
     public boolean equals(Object other) {
         if (other == null || !(other instanceof GLFGenotypeCall))

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

@@ -4,8 +4,6 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.genotype.*;
 
-import java.util.Arrays;
-
 
 /**
  * @author ebanks
@@ -20,14 +18,12 @@ public class VCFGenotypeCall extends AlleleConstrainedGenotype implements Genoty
 
     private ReadBackedPileup mPileup = null;
     private int mCoverage = 0;
-    private double[] mPosteriors;
+    private double mNegLog10PError = -1;
 
     private Variation mVariation = null;
 
-    // the reference genotype, the best genotype, and the next best genotype, lazy loaded
+    // the best genotype
-    private DiploidGenotype mRefGenotype = null;
+    private DiploidGenotype mGenotype = null;
-    private DiploidGenotype mBestGenotype = null;
-    private DiploidGenotype mNextGenotype = null;
 
     // the sample name, used to propulate the SampleBacked interface
     private String mSampleName;
@@ -38,44 +34,30 @@ public class VCFGenotypeCall extends AlleleConstrainedGenotype implements Genoty
         mLocation = loc;
 
         // fill in empty data
-        mPosteriors = new double[10];
+        mGenotype = DiploidGenotype.createHomGenotype(ref);
-        Arrays.fill(mPosteriors, Double.MIN_VALUE);
         mSampleName = "";
     }
 
-    public VCFGenotypeCall(char ref, GenomeLoc loc, String genotype, double negLog10PError, int coverage, String sample) {
+    public VCFGenotypeCall(char ref, GenomeLoc loc, DiploidGenotype genotype, double negLog10PError, int coverage, String sample) {
         super(ref);
         mRefBase = ref;
         mLocation = loc;
-        mBestGenotype = DiploidGenotype.unorderedValueOf(genotype);
+        mGenotype = genotype;
-        mRefGenotype = DiploidGenotype.createHomGenotype(ref);
+        mNegLog10PError = negLog10PError;
-        mSampleName = sample;
         mCoverage = coverage;
-
+        mSampleName = sample;
-        // set general posteriors to min double value
-        mPosteriors = new double[10];
-        Arrays.fill(mPosteriors, Double.MIN_VALUE);
-
-        // set the ref to PError
-        mPosteriors[mRefGenotype.ordinal()] = -1.0 * negLog10PError;
-
-        // set the best genotype to zero (need to do this after ref in case ref=best)
-        mPosteriors[mBestGenotype.ordinal()] = 0.0;
-
-        // choose a smart next best genotype and set it to PError
-        if ( mBestGenotype == mRefGenotype )
-            mNextGenotype = DiploidGenotype.valueOf(BaseUtils.simpleComplement(genotype));
-        else
-            mNextGenotype = mRefGenotype;
-        mPosteriors[mNextGenotype.ordinal()] = -1.0 * negLog10PError;
     }
 
     public void setPileup(ReadBackedPileup pileup) {
         mPileup = pileup;
     }
 
-    public void setPosteriors(double[] posteriors) {
+    public void setGenotype(DiploidGenotype genotype) {
-        mPosteriors = posteriors;
+        mGenotype = genotype;
+    }
+
+    public void setNegLog10PError(double negLog10PError) {
+        mNegLog10PError = negLog10PError;
     }
 
     public void setVariation(Variation variation) {
@@ -89,53 +71,21 @@ public class VCFGenotypeCall extends AlleleConstrainedGenotype implements Genoty
 
     @Override
     public boolean equals(Object other) {
-        lazyEval();
 
-        if (other == null)
+        if ( other == null || !(other instanceof VCFGenotypeCall) )
             return false;
-        if (other instanceof VCFGenotypeCall) {
-            VCFGenotypeCall otherCall = (VCFGenotypeCall) other;
 
-            if (!this.mBestGenotype.equals(otherCall.mBestGenotype))
+        VCFGenotypeCall otherCall = (VCFGenotypeCall) other;
-                return false;
+
-            return (this.mRefBase == otherCall.mRefBase && this.mLocation.equals(otherCall.mLocation));
+        return mGenotype.equals(otherCall.mGenotype) &&
-        }
+               mNegLog10PError == otherCall.mNegLog10PError &&
-        return false;
+               mLocation.equals(otherCall.mLocation) &&
+               mRefBase == otherCall.mRefBase;
     }
 
     public String toString() {
-        lazyEval();
+        return String.format("%s best=%s ref=%s depth=%d negLog10PError=%.2f",
-        return String.format("%s best=%s cmp=%s ref=%s depth=%d negLog10PError=%.2f",
+                             getLocation(), mGenotype, mRefBase, getReadCount(), getNegLog10PError());
-                             getLocation(), mBestGenotype, mRefGenotype, mRefBase, getReadCount(), getNegLog10PError());
-    }
-
-    private void lazyEval() {
-        if (mBestGenotype == null) {
-            char ref = this.getReference();
-            char alt = this.getAlternateAllele();
-
-            mRefGenotype = DiploidGenotype.createHomGenotype(ref);
-
-            // if we are constrained to a single alternate allele, use only that one
-            if ( alt != AlleleConstrainedGenotype.NO_CONSTRAINT ) {
-                DiploidGenotype hetGenotype = ref < alt ? DiploidGenotype.valueOf(String.valueOf(ref) + String.valueOf(alt)) : DiploidGenotype.valueOf(String.valueOf(alt) + String.valueOf(ref));
-                DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
-                boolean hetOverHom = mPosteriors[hetGenotype.ordinal()] > mPosteriors[homGenotype.ordinal()];
-                boolean hetOverRef = mPosteriors[hetGenotype.ordinal()] > mPosteriors[mRefGenotype.ordinal()];
-                boolean homOverRef = mPosteriors[homGenotype.ordinal()] > mPosteriors[mRefGenotype.ordinal()];
-                if ( hetOverHom ) {
-                    mBestGenotype = (hetOverRef ? hetGenotype : mRefGenotype);
-                    mNextGenotype = (!hetOverRef ? hetGenotype : (homOverRef ? homGenotype : mRefGenotype));
-                } else {
-                    mBestGenotype = (homOverRef ? homGenotype : mRefGenotype);
-                    mNextGenotype = (!homOverRef ? homGenotype : (hetOverRef ? hetGenotype : mRefGenotype));
-                }
-            } else {
-                Integer sorted[] = Utils.SortPermutation(mPosteriors);
-                mBestGenotype = DiploidGenotype.values()[sorted[DiploidGenotype.values().length - 1]];
-                mNextGenotype = DiploidGenotype.values()[sorted[DiploidGenotype.values().length - 2]];
-            }
-        }
     }
 
     /**
@@ -144,25 +94,12 @@ public class VCFGenotypeCall extends AlleleConstrainedGenotype implements Genoty
      * @return get the one minus error value
      */
     public double getNegLog10PError() {
-        return Math.abs(mPosteriors[getBestGenotype().ordinal()] - mPosteriors[getNextBest().ordinal()]);
+        return mNegLog10PError;
     }
 
     // get the best genotype
     protected DiploidGenotype getBestGenotype() {
-        lazyEval();
+        return mGenotype;
-        return mBestGenotype;
-    }
-
-    // get the alternate genotype
-    private DiploidGenotype getNextBest() {
-        lazyEval();
-        return mNextGenotype;
-    }
-
-    // get the ref genotype
-    private DiploidGenotype getRefGenotype() {
-        lazyEval();
-        return mRefGenotype;
     }
 
     /**
@@ -238,11 +175,14 @@ public class VCFGenotypeCall extends AlleleConstrainedGenotype implements Genoty
     public Variation toVariation(char ref) {
         if ( mVariation == null ) {
             VCFVariationCall var = new VCFVariationCall(ref, mLocation, isVariant() ? Variation.VARIANT_TYPE.SNP : Variation.VARIANT_TYPE.REFERENCE);
-            double confidence = Math.abs(mPosteriors[getBestGenotype().ordinal()] - mPosteriors[getRefGenotype().ordinal()]);
+            var.setConfidence(10 * mNegLog10PError);
-            var.setConfidence(confidence);
+            if ( !mGenotype.isHomRef(ref) ) {
-            if ( isVariant() )
+                if ( mGenotype.base1 != ref )
-                var.addAlternateAllele(Character.toString(mBestGenotype.base1 != ref ? mBestGenotype.base1 : mBestGenotype.base2));
+                    var.addAlternateAllele(Character.toString(mGenotype.base1));
-            mVariation = var;    
+                if ( mGenotype.isHet() && mGenotype.base2 != ref )
+                    var.addAlternateAllele(Character.toString(mGenotype.base2));
+            }
+            mVariation = var;
         }
         return mVariation;
     }
@@ -274,15 +214,6 @@ public class VCFGenotypeCall extends AlleleConstrainedGenotype implements Genoty
         return mRefBase;
     }
 
-    /**
-     * get the posteriors
-     *
-     * @return the posteriors
-     */
-    public double[] getPosteriors() {
-        return mPosteriors;
-    }
-
     /**
      * @return returns the sample name for this genotype
      */

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

@@ -42,7 +42,7 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
     private char mReferenceBase;
     // our location
     private GenomeLoc mLoc;
-    // our id; set to '.' if not available
+    // our id
     private String mID;
     // the alternate bases
     private final List<VCFGenotypeEncoding> mAlts = new ArrayList<VCFGenotypeEncoding>();

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

@@ -179,6 +179,8 @@ public class VCFUtils {
         if ( freqsSeen > 0 )
             infoFields.put(VCFRecord.ALLELE_FREQUENCY_KEY, String.format("%.2f", (totalFreq/(double)freqsSeen)));
 
+        // TODO -- "." and "0" are wrong -- need to use values from the records
+
         return new VCFRecord(params.getReferenceBase(),
                 params.getContig(),
                 params.getPosition(),

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -47,7 +47,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1PointEM() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("8f9ee611603dc75c7ca8b15d81000a82"));
+                Arrays.asList("ad00b255c83fe43213758b280646e4b4"));
         executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
     }
 
@@ -55,7 +55,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot2PointEM() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("a8979577debf9c8d7ea4a40ee1a0f1ef"));
+                Arrays.asList("e709714e288c508f79c1ffc5cdbe9cca"));
         executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
     }
 
@@ -68,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testPooled1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1,
-                Arrays.asList("253aba7ce0af7be4104dd275873a541d"));
+                Arrays.asList("2214983d4ae3a19bc16e7cb89fc3128f"));
         executeTest("testPooled1", spec);
     }
 
@@ -81,7 +81,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("1be2ce6ac40bdaf3d8f264f6d73c84ae"));
+                Arrays.asList("9e98eba56add9989e2d40834efc8c803"));
         executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
     }
 
@@ -89,7 +89,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot2Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("8f92a56da4bd56b8755e9db89c31bfff"));
+                Arrays.asList("fe1077636feb41c69f7c4f64147e2bba"));
         executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
     }
 
@@ -97,7 +97,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSingleSamplePilot2Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("67913655a8063f4deb9a6138f0844ddd"));
+                Arrays.asList("6a739a0acb620aeed5d8e0de7b59877a"));
         executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
     }
 
@@ -105,7 +105,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testGenotypeModeJoint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -genotype -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,001,000 -bm empirical -gm JOINT_ESTIMATE -confidence 70", 1,
-                Arrays.asList("d51760ad01195ab299925595c6f62bb4"));
+                Arrays.asList("85fbcdd816ecc1d9686df244a6e039dd"));
         executeTest("testGenotypeMode - Joint Estimate", spec);
     }
 
@@ -113,7 +113,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testAllBasesModeJoint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -all_bases -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,001,000 -bm empirical -gm JOINT_ESTIMATE -confidence 70", 1,
-                Arrays.asList("2322d3ebf09ebf901fbcb653119d0b47"));
+                Arrays.asList("f871576cf49e7a83a0f6b5580b0178c2"));
         executeTest("testAllBasesMode - Joint Estimate", spec);
     }