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    private final boolean useAlleleFromVCF;

    private final double[] likelihoodSums = new double[4];

    private final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap;

    protected SNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {

        super(UAC, logger);

        useAlleleFromVCF = UAC.genotypingOutputMode == GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES;

        perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();

    }

    public VariantContext getLikelihoods(final RefMetaDataTracker tracker,

                                         final ReferenceContext ref,

                                         final Map<String, AlignmentContext> contexts,

                                         final AlignmentContextUtils.ReadOrientation contextType,

                                         final List<Allele> allAllelesToUse,

                                         final boolean useBAQedPileup,

                                         final GenomeLocParser locParser,

                                         final Map<String, PerReadAlleleLikelihoodMap> sampleLikelihoodMap) {

        sampleLikelihoodMap.clear(); // not used in SNP model, sanity check to delete any older data

        final byte refBase = ref.getBase();

        final int indexOfRefBase = BaseUtils.simpleBaseToBaseIndex(refBase);

        // handle non-standard reference bases

        if ( indexOfRefBase == -1 )

            return null;

        final Allele refAllele = Allele.create(refBase, true);

        // calculate the GLs

        ArrayList<SampleGenotypeData> GLs = new ArrayList<SampleGenotypeData>(contexts.size());

        for ( Map.Entry<String, AlignmentContext> sample : contexts.entrySet() ) {

        // Down-sample with bias according to the contamination level (global or per file)

            ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup();

            final Double contamination =  UAC.getSampleContamination().get(sample.getKey());

            if( contamination > 0.0 ) //no need to enter if no contamination reduction

                pileup = perReadAlleleLikelihoodMap.createPerAlleleDownsampledBasePileup(pileup, contamination);

            if ( useBAQedPileup )

                pileup = createBAQedPileup(pileup);

            // create the GenotypeLikelihoods object

            final DiploidSNPGenotypeLikelihoods GL = new DiploidSNPGenotypeLikelihoods(UAC.PCR_error);

            final int nGoodBases = GL.add(pileup, true, true, UAC.MIN_BASE_QUALTY_SCORE);

            if ( nGoodBases > 0 )

                GLs.add(new SampleGenotypeData(sample.getKey(), GL, getFilteredDepth(pileup)));

        }

        // start making the VariantContext

        final GenomeLoc loc = ref.getLocus();

        final List<Allele> alleles = new ArrayList<Allele>();

        alleles.add(refAllele);

        final VariantContextBuilder builder = new VariantContextBuilder("UG_call", loc.getContig(), loc.getStart(), loc.getStop(), alleles);

        // find the alternate allele(s) that we should be using

        if ( allAllelesToUse != null ) {

            alleles.addAll(allAllelesToUse.subList(1,allAllelesToUse.size()));   // this includes ref allele

        } else if ( useAlleleFromVCF ) {

            final VariantContext vc = GenotypingGivenAllelesUtils.composeGivenAllelesVariantContextFromRod(tracker, ref.getLocus(), true, logger, UAC.alleles);

            // ignore places where we don't have a SNP

            if ( vc == null || !vc.isSNP() )

                return null;

            // make sure a user isn't passing the REF base in as an ALT

            if ( vc.hasAlternateAllele(refAllele, true) )

                throw new UserException.BadInput("Alternate allele '" + (char)refBase + "' passed in is the same as the reference at location " + vc.getChr() + ":" + vc.getStart());

            alleles.addAll(vc.getAlternateAlleles());

        } else {

            alleles.addAll(determineAlternateAlleles(refBase, GLs));

            // if there are no non-ref alleles...

            if ( alleles.size() == 1 ) {

                // if we only want variants, then we don't need to calculate genotype likelihoods

                if ( UAC.outputMode == OutputMode.EMIT_VARIANTS_ONLY )

                    return builder.make();

                else

                    // otherwise, choose any alternate allele (it doesn't really matter)

                    alleles.add(Allele.create(BaseUtils.baseIndexToSimpleBase(indexOfRefBase == 0 ? 1 : 0)));

             }

        }

        // create the alternate alleles and the allele ordering (the ordering is crucial for the GLs)

        final int numAlleles = alleles.size();

        final int numAltAlleles = numAlleles - 1;

        final int[] alleleOrdering = new int[numAlleles];

        int alleleOrderingIndex = 0;

        int numLikelihoods = 0;

        for ( Allele allele : alleles ) {

            alleleOrdering[alleleOrderingIndex++] = BaseUtils.simpleBaseToBaseIndex(allele.getBases()[0]);

            numLikelihoods += alleleOrderingIndex;

        }

        builder.alleles(alleles);

        // create the PL ordering to use based on the allele ordering.

        final int[] PLordering = new int[numLikelihoods];

        for ( int i = 0; i <= numAltAlleles; i++ ) {

            for ( int j = i; j <= numAltAlleles; j++ ) {

                // As per the VCF spec: "the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j.

                // In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc."

                PLordering[(j * (j+1) / 2) + i] = DiploidGenotype.createDiploidGenotype(alleleOrdering[i], alleleOrdering[j]).ordinal();

            }

        }

        // create the genotypes; no-call everyone for now

        final GenotypesContext genotypes = GenotypesContext.create();

        final int ploidy = UAC.genotypeArgs.samplePloidy;

        final List<Allele> noCall = GATKVariantContextUtils.noCallAlleles(ploidy);

        for ( SampleGenotypeData sampleData : GLs ) {

            final double[] allLikelihoods = sampleData.GL.getLikelihoods();

            final double[] myLikelihoods = new double[numLikelihoods];

            for ( int i = 0; i < numLikelihoods; i++ )

                myLikelihoods[i] = allLikelihoods[PLordering[i]];

            // normalize in log space so that max element is zero.

            final GenotypeBuilder gb = new GenotypeBuilder(sampleData.name);

            final double[] genotypeLikelihoods = MathUtils.normalizeFromLog10(myLikelihoods, false, true);

            gb.PL(genotypeLikelihoods);

            gb.DP(sampleData.depth);

            gb.alleles(noCall);

            if (UAC.annotateAllSitesWithPLs)

                gb.attribute(UnifiedGenotypingEngine.PL_FOR_ALL_SNP_ALLELES_KEY,GenotypeLikelihoods.fromLog10Likelihoods(MathUtils.normalizeFromLog10(allLikelihoods, false, true)));

            genotypes.add(gb.make());

        }

        return builder.genotypes(genotypes).make();

    }

   

    // determines the alleles to use

    protected List<Allele> determineAlternateAlleles(final byte ref, final List<SampleGenotypeData> sampleDataList) {

        final int baseIndexOfRef = BaseUtils.simpleBaseToBaseIndex(ref);

        final int PLindexOfRef = DiploidGenotype.createDiploidGenotype(ref, ref).ordinal();

        for ( int i = 0; i < 4; i++ )

            likelihoodSums[i] = 0.0;

       

        // based on the GLs, find the alternate alleles with enough probability

        for ( SampleGenotypeData sampleData : sampleDataList ) {

            final double[] likelihoods = sampleData.GL.getLikelihoods();

            final int PLindexOfBestGL = MathUtils.maxElementIndex(likelihoods);

            if ( PLindexOfBestGL != PLindexOfRef ) {

                GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindexOfBestGL);

                if ( alleles.alleleIndex1 != baseIndexOfRef )

                    likelihoodSums[alleles.alleleIndex1] += likelihoods[PLindexOfBestGL] - likelihoods[PLindexOfRef];

                // don't double-count it

                if ( alleles.alleleIndex2 != baseIndexOfRef && alleles.alleleIndex2 != alleles.alleleIndex1 )

                    likelihoodSums[alleles.alleleIndex2] += likelihoods[PLindexOfBestGL] - likelihoods[PLindexOfRef];

            }

        }

        final List<Allele> allelesToUse = new ArrayList<Allele>(3);

        for ( int i = 0; i < 4; i++ ) {

            if ( likelihoodSums[i] > 0.0 )

                allelesToUse.add(Allele.create(BaseUtils.baseIndexToSimpleBase(i), false));

        }

        return allelesToUse;

    }

    public ReadBackedPileup createBAQedPileup( final ReadBackedPileup pileup ) {

        final List<PileupElement> BAQedElements = new ArrayList<PileupElement>();

        for( final PileupElement PE : pileup ) {

            final PileupElement newPE = new BAQedPileupElement( PE );

            BAQedElements.add( newPE );

        }

        return new ReadBackedPileupImpl( pileup.getLocation(), BAQedElements );

    }

        public BAQedPileupElement( final PileupElement PE ) {

            super(PE);

        }

        @Override

        public byte getQual() {

            if ( isDeletion() )

                return super.getQual();

            else

                return BAQ.calcBAQFromTag(getRead(), offset, true);

        }

    }

    private static class SampleGenotypeData {

        public final String name;

        public final DiploidSNPGenotypeLikelihoods GL;

        public final int depth;

        public SampleGenotypeData(final String name, final DiploidSNPGenotypeLikelihoods GL, final int depth) {

            this.name = name;

            this.GL = GL;

            this.depth = depth;

        }

    }

}