Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

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

@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
+import java.util.List;
 import java.util.Map;
 
 
@@ -81,19 +82,19 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
       * @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 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,
+     public abstract VariantContext getLikelihoods(final RefMetaDataTracker tracker,
-                                                   ReferenceContext ref,
+                                                   final ReferenceContext ref,
-                                                   Map<String, AlignmentContext> contexts,
+                                                   final Map<String, AlignmentContext> contexts,
-                                                   AlignmentContextUtils.ReadOrientation contextType,
+                                                   final AlignmentContextUtils.ReadOrientation contextType,
-                                                   GenotypePriors priors,
+                                                   final GenotypePriors priors,
-                                                   Allele alternateAlleleToUse,
+                                                   final List<Allele> alternateAllelesToUse,
-                                                   boolean useBAQedPileup,
+                                                   final boolean useBAQedPileup,
-                                                   GenomeLocParser locParser);
+                                                   final GenomeLocParser locParser);
 
 
     protected int getFilteredDepth(ReadBackedPileup pileup) {

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

@@ -284,13 +284,14 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
 
     private final static EnumSet<VariantContext.Type> allowableTypes = EnumSet.of(VariantContext.Type.INDEL, VariantContext.Type.MIXED);
 
-    public VariantContext getLikelihoods(RefMetaDataTracker tracker,
+    public VariantContext getLikelihoods(final RefMetaDataTracker tracker,
-                                         ReferenceContext ref,
+                                         final ReferenceContext ref,
-                                         Map<String, AlignmentContext> contexts,
+                                         final Map<String, AlignmentContext> contexts,
-                                         AlignmentContextUtils.ReadOrientation contextType,
+                                         final AlignmentContextUtils.ReadOrientation contextType,
-                                         GenotypePriors priors,
+                                         final GenotypePriors priors,
-                                         Allele alternateAlleleToUse,
+                                         final List<Allele> alternateAllelesToUse,
-                                         boolean useBAQedPileup, GenomeLocParser locParser) {
+                                         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 class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
                                          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 class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         }
 
         // find the alternate allele(s) that we should be using
-        if ( alternateAlleleToUse != null ) {
+        if ( alternateAllelesToUse != null ) {
-            alleles.add(alternateAlleleToUse);
+            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 class UnifiedGenotyperEngine {
     // ---------------------------------------------------------------------------------------------------------
 
     // 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 @@ public class UnifiedGenotyperEngine {
             //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 @@ public class UnifiedGenotyperEngine {
             //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);