Fixes for SLOD: 1) didn't work properly for multi-allelics (randomly …

…chose an allele, possibly one that wasn't genotyped in the full context); 2) in cases when there were more alt alleles than the max allowed and the user is calculating SB, we would recompute the best alt alleles(s); 3) for some reason, we were recomputing the LOD for the full context when we'd already done that. Given that this passes integration tests on my end, this should be the last commit before the release.

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

@@ -38,6 +38,7 @@
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
+import java.util.List;
 import java.util.Map;
 
 
@@ -76,24 +77,24 @@ protected GenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Log
      /**
       * Can be overridden by concrete subclasses
       *
-      * @param tracker              rod data
-      * @param ref                  reference context
-      * @param contexts             stratified alignment contexts
-      * @param contextType          stratified context type
-      * @param priors               priors to use for GLs
-      * @param alternateAlleleToUse the alternate allele to use, null if not set
-      * @param useBAQedPileup       should we use the BAQed pileup or the raw one?
-      * @param locParser            Genome Loc Parser
+      * @param tracker               rod data
+      * @param ref                   reference context
+      * @param contexts              stratified alignment contexts
+      * @param contextType           stratified context type
+      * @param priors                priors to use for GLs
+      * @param alternateAllelesToUse the alternate allele to use, null if not set
+      * @param useBAQedPileup        should we use the BAQed pileup or the raw one?
+      * @param locParser             Genome Loc Parser
       * @return variant context where genotypes are no-called but with GLs
       */
-     public abstract VariantContext getLikelihoods(RefMetaDataTracker tracker,
-                                                   ReferenceContext ref,
-                                                   Map<String, AlignmentContext> contexts,
-                                                   AlignmentContextUtils.ReadOrientation contextType,
-                                                   GenotypePriors priors,
-                                                   Allele alternateAlleleToUse,
-                                                   boolean useBAQedPileup,
-                                                   GenomeLocParser locParser);
+     public abstract VariantContext getLikelihoods(final RefMetaDataTracker tracker,
+                                                   final ReferenceContext ref,
+                                                   final Map<String, AlignmentContext> contexts,
+                                                   final AlignmentContextUtils.ReadOrientation contextType,
+                                                   final GenotypePriors priors,
+                                                   final List<Allele> alternateAllelesToUse,
+                                                   final boolean useBAQedPileup,
+                                                   final GenomeLocParser locParser);
 
 
     protected int getFilteredDepth(ReadBackedPileup pileup) {

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

@@ -284,13 +284,14 @@ else if (p.isDeletion()) {
 
     private final static EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.INDEL, VariantContext.Type.MIXED);
 
-    public VariantContext getLikelihoods(RefMetaDataTracker tracker,
-                                         ReferenceContext ref,
-                                         Map<String, AlignmentContext> contexts,
-                                         AlignmentContextUtils.ReadOrientation contextType,
-                                         GenotypePriors priors,
-                                         Allele alternateAlleleToUse,
-                                         boolean useBAQedPileup, GenomeLocParser locParser) {
+    public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
+                                         final ReferenceContext ref,
+                                         final Map<String, AlignmentContext> contexts,
+                                         final AlignmentContextUtils.ReadOrientation contextType,
+                                         final GenotypePriors priors,
+                                         final List<Allele> alternateAllelesToUse,
+                                         final boolean useBAQedPileup,
+                                         final GenomeLocParser locParser) {
 
         if (tracker == null)
             return null;

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

@@ -64,7 +64,7 @@ public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
                                          final Map<String, AlignmentContext> contexts,
                                          final AlignmentContextUtils.ReadOrientation contextType,
                                          final GenotypePriors priors,
-                                         final Allele alternateAlleleToUse,
+                                         final List<Allele> alternateAllelesToUse,
                                          final boolean useBAQedPileup,
                                          final GenomeLocParser locParser) {
 
@@ -95,8 +95,8 @@ public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
         }
 
         // find the alternate allele(s) that we should be using
-        if ( alternateAlleleToUse != null ) {
-            alleles.add(alternateAlleleToUse);
+        if ( alternateAllelesToUse != null ) {
+            alleles.addAll(alternateAllelesToUse);
         } else if ( useAlleleFromVCF ) {
             final VariantContext vc = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, ref.getLocus(), true, logger, UAC.alleles);
 

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

@@ -237,14 +237,14 @@ public VariantCallContext calculateGenotypes(RefMetaDataTracker tracker, Referen
     // ---------------------------------------------------------------------------------------------------------
 
     // private method called by both UnifiedGenotyper and UGCalcLikelihoods entry points into the engine
-    private VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, Map<String, AlignmentContext> stratifiedContexts, AlignmentContextUtils.ReadOrientation type, Allele alternateAlleleToUse, boolean useBAQedPileup, final GenotypeLikelihoodsCalculationModel.Model model) {
+    private VariantContext calculateLikelihoods(RefMetaDataTracker tracker, ReferenceContext refContext, Map<String, AlignmentContext> stratifiedContexts, AlignmentContextUtils.ReadOrientation type, List<Allele> alternateAllelesToUse, boolean useBAQedPileup, final GenotypeLikelihoodsCalculationModel.Model model) {
 
         // initialize the data for this thread if that hasn't been done yet
         if ( glcm.get() == null ) {
             glcm.set(getGenotypeLikelihoodsCalculationObject(logger, UAC));
         }
 
-        return glcm.get().get(model).getLikelihoods(tracker, refContext, stratifiedContexts, type, getGenotypePriors(model), alternateAlleleToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser);
+        return glcm.get().get(model).getLikelihoods(tracker, refContext, stratifiedContexts, type, getGenotypePriors(model), alternateAllelesToUse, useBAQedPileup && BAQEnabledOnCMDLine, genomeLocParser);
     }
 
     private VariantCallContext generateEmptyContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, AlignmentContext rawContext) {
@@ -398,16 +398,14 @@ else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_M
             //final boolean DEBUG_SLOD = false;
 
             // the overall lod
-            VariantContext vcOverall = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, vc.getAlternateAllele(0), false, model);
-            clearAFarray(AFresult.log10AlleleFrequencyLikelihoods);
-            clearAFarray(AFresult.log10AlleleFrequencyPosteriors);
-            afcm.get().getLog10PNonRef(vcOverall, getAlleleFrequencyPriors(model), AFresult);
             //double overallLog10PofNull = AFresult.log10AlleleFrequencyPosteriors[0];
             double overallLog10PofF = MathUtils.log10sumLog10(AFresult.log10AlleleFrequencyPosteriors[0], 0);
             //if ( DEBUG_SLOD ) System.out.println("overallLog10PofF=" + overallLog10PofF);
 
+            List<Allele> alternateAllelesToUse = builder.make().getAlternateAlleles();
+
             // the forward lod
-            VariantContext vcForward = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.FORWARD, vc.getAlternateAllele(0), false, model);
+            VariantContext vcForward = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.FORWARD, alternateAllelesToUse, false, model);
             clearAFarray(AFresult.log10AlleleFrequencyLikelihoods);
             clearAFarray(AFresult.log10AlleleFrequencyPosteriors);
             afcm.get().getLog10PNonRef(vcForward, getAlleleFrequencyPriors(model), AFresult);
@@ -417,7 +415,7 @@ else if ( UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_M
             //if ( DEBUG_SLOD ) System.out.println("forwardLog10PofNull=" + forwardLog10PofNull + ", forwardLog10PofF=" + forwardLog10PofF);
 
             // the reverse lod
-            VariantContext vcReverse = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.REVERSE, vc.getAlternateAllele(0), false, model);
+            VariantContext vcReverse = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.REVERSE, alternateAllelesToUse, false, model);
             clearAFarray(AFresult.log10AlleleFrequencyLikelihoods);
             clearAFarray(AFresult.log10AlleleFrequencyPosteriors);
             afcm.get().getLog10PNonRef(vcReverse, getAlleleFrequencyPriors(model), AFresult);