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package org.broadinstitute.gatk.tools.walkers.genotyper;

import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.GenotypeLikelihoods;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.collections.IntMaxHeap;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;

/**
 * Helper to calculate genotype likelihoods given a ploidy and an allele count (number of possible distinct alleles).
 *
 * <p>
 *     Notice that for performance this class is thread-unsafe an so it cannot be shared between thread in a multi-thread run.
 * </p>
 *
 * @author Valentin Ruano-Rubio &lt;valentin@broadinstitute.org&gt;
 */
public class GenotypeLikelihoodCalculator {

    /**
     * Maximum number of components (or distinct alleles) for any genotype with this calculator ploidy and allele count.
     */
    private int maximumDistinctAllelesInGenotype;

    /**
     * Offset table for this calculator.
     *
     * <p>
     *     This is a shallow copy of {@link GenotypeLikelihoodCalculators#alleleFirstGenotypeOffsetByPloidy} when the calculator was created
     *     thus it follows the same format as that array. Please refer to its documentation.
     * </p>
     *
     * <p>You can assume that this offset table contain at least (probably more) the numbers corresponding to the allele count and ploidy for this calculator.
     * However since it might have more than that and so you must use {@link #alleleCount} and {@link #ploidy} when
     * iterating through this array rather that its length or the length of its components.</p>.
     */
    private final int[][] alleleFirstGenotypeOffsetByPloidy;

    /**
     * Genotype table for this calculator.
     *
     * <p>It is ensure that it contains all the genotypes for this calculator ploidy and allele count, maybe more. For
     * that reason you must use {@link #genotypeCount} when iterating through this array and not relay on its length.</p>
     */
    private final GenotypeAlleleCounts[] genotypeAlleleCounts;

    /**
     * Number of genotypes given this calculator {@link #ploidy} and {@link #alleleCount}.
     */
    private final int genotypeCount;

    /**
     * Number of genotyping alleles for this calculator.
     */
    private final int alleleCount;

    /**
     * Ploidy for this calculator.
     */
    private final int ploidy;

    /**
     * Max-heap for integers used for this calculator internally.
     */
    private final IntMaxHeap alleleHeap;

    /**
     * Cache of the last genotype-allele-count requested using {@link #genotypeAlleleCountsAt(int)}, when it
     * goes beyond the maximum genotype-allele-count static capacity. Check on that method documentation for details.
     */
    private transient GenotypeAlleleCounts lastOverheadCounts;

    /**
     * Buffer used as a temporary container for likelihood components for genotypes stratified by alleles, allele frequency and reads.
     *
     * <p>To improve performance we use a 1-dimensional array to implement a 3-dimensional one as some of those dimension
     * have typically very low depths (allele and allele frequency)</p>
     *
     * <p>
     *     The value contained in position <code>[a][f][r] == log10Lk(read[r] | allele[a]) + log10(f) </code>. Exception is
     *     for f == 0 whose value is undefined (in practice 0.0) and never used.
     * </p>
     *
     * <p>
     *     It is indexed by read, then by allele and then by the number of copies of the allele. For the latter
     *     there are as many entries as the ploidy of the calculator + 1 (to accommodate zero copies although is
     *     never used in practice).
     * </p>
     */
    private double[] readAlleleLikelihoodByAlleleCount = null;

    /**
     * Buffer used as a temporary container for likelihood components for genotypes stratified by reads.
     *
     * <p>
     *     It is indexed by genotype index and then by read index. The read capacity is increased as needed by calling
     *     {@link #ensureReadCapacity(int) ensureReadCapacity}.
     * </p>
     */
    private final double[][] readLikelihoodsByGenotypeIndex;

    /**
     * Indicates how many reads the calculator supports.
     *
     * <p>This figure is increased dynamically as per the
     * calculation request calling {@link #ensureReadCapacity(int) ensureReadCapacity}.<p/>
     */
    private int readCapacity = -1;

    /**
     * Caches the log10 of the first few integers up to the ploidy supported by the calculator.
     * <p>This is in fact a shallow copy if {@link GenotypeLikelihoodCalculators#ploidyLog10}</p> and is not meant to be modified by
     * this class. </p>
     */
    private final double[] log10;

    /**
     * Buffer field use as a temporal container for sorted allele counts when calculating the likelihood of a
     * read in a genotype.
     * <p>
     *      This array follows the same format as {@link GenotypeAlleleCounts#sortedAlleleCounts}. Each component in the
     *      genotype takes up two positions in the array where the first indicate the allele index and the second its frequency in the
     *      genotype. Only non-zero frequency alleles are represented, taking up the first positions of the array.
     * </p>
     *
     * <p>
     *     This array is sized so that it can accommodate the maximum possible number of distinct alleles in any
     *     genotype supported by the calculator, value stored in {@link #maximumDistinctAllelesInGenotype}.
     * </p>
     */
    private final int[] genotypeAllelesAndCounts;

    /**
     * Buffer field use as a temporal container for component likelihoods when calculating the likelihood of a
     * read in a genotype. It is stratified by read and the allele component of the genotype likelihood... that is
     * the part of the likelihood sum that correspond to a particular allele in the genotype.
     *
     * <p>
     *     It is implemented in a 1-dimensional array since typically one of the dimensions is rather small. Its size
     *     is equal to {@link #readCapacity} times {@link #maximumDistinctAllelesInGenotype}.
     * </p>
     *
     * <p>
     *     More concretely [r][i] == log10Lk(read[r] | allele[i]) + log(freq[i]) where allele[i] is the ith allele
     *     in the genotype of interest and freq[i] is the number of times it occurs in that genotype.
     * </p>
     */
    private double[] readGenotypeLikelihoodComponents;

    /**
     * Creates a new calculator providing its ploidy and number of genotyping alleles.
     */
    protected GenotypeLikelihoodCalculator(final int ploidy, final int alleleCount,
                                          final int[][] alleleFirstGenotypeOffsetByPloidy,
                                          final GenotypeAlleleCounts[][] genotypeTableByPloidy,
                                          final double[] ploidyLog10) {
        this.alleleFirstGenotypeOffsetByPloidy = alleleFirstGenotypeOffsetByPloidy;
        genotypeAlleleCounts = genotypeTableByPloidy[ploidy];
        this.alleleCount = alleleCount;
        this.ploidy = ploidy;
        genotypeCount = this.alleleFirstGenotypeOffsetByPloidy[ploidy][alleleCount];
        if (genotypeCount == GenotypeLikelihoodCalculators.GENOTYPE_COUNT_OVERFLOW)
            throw new IllegalArgumentException(
                    String.format("the combination of ploidy (%s) and number of alleles (%s) results in a very large number of genotypes (> %s). You need to limit ploidy or the number of alternative alleles to analyze this locus",
                            ploidy,alleleCount,Integer.MAX_VALUE));
        alleleHeap = new IntMaxHeap(ploidy);
        readLikelihoodsByGenotypeIndex = new double[genotypeCount][];
        log10 = ploidyLog10;
        // The number of possible components is limited by distinct allele count and ploidy.
        maximumDistinctAllelesInGenotype = Math.min(ploidy, alleleCount);
        genotypeAllelesAndCounts = new int[maximumDistinctAllelesInGenotype << 1];
    }

    /**
     * Makes sure that temporal arrays and matrices are prepared for a number of reads to process.
     * @param requestedCapacity number of read that need to be processed.
     */
    public void ensureReadCapacity(final int requestedCapacity) {
        if (requestedCapacity < 0)
            throw new IllegalArgumentException("illegal capacity value");
        if (readCapacity == -1) { // first time call.
            final int minimumCapacity = Math.max(requestedCapacity,10); // Never go too small, 10 is the minimum.
            readAlleleLikelihoodByAlleleCount = new double[minimumCapacity * alleleCount * (ploidy+1)];
            for (int i = 0; i < genotypeCount; i++)
                readLikelihoodsByGenotypeIndex[i] = new double[minimumCapacity];
            readGenotypeLikelihoodComponents = new double[ploidy * minimumCapacity];
            readCapacity = minimumCapacity;
        } else if (readCapacity < requestedCapacity) {
            final int doubleCapacity = (requestedCapacity << 1);
            readAlleleLikelihoodByAlleleCount = new double[doubleCapacity * alleleCount * (ploidy+1)];
            for (int i = 0; i < genotypeCount; i++)
                readLikelihoodsByGenotypeIndex[i] = new double[doubleCapacity];
            readGenotypeLikelihoodComponents = new double[maximumDistinctAllelesInGenotype * doubleCapacity];
            readCapacity = doubleCapacity;
        }
    }

    /**
     * Give a list of alleles, returns the likelihood array index.
     *
     * <p>This operation is <b>thread-unsafe</b>.</p>
     *
     * @param alleleIndices the indices of the alleles in the genotype, there should be as many repetition of an
     *                      index as copies of that allele in the genotype. Allele indices do not need to be sorted in
     *                      any particular way.
     *
     * @return never {@code null}.
     */
    public int allelesToIndex(final int... alleleIndices) {
        // Special case ploidy == 0.
        if (ploidy == 0) return 0;

        alleleHeap.clear();
        alleleHeap.add(alleleIndices);
        return alleleHeapToIndex();
    }

    /**
     * Returns the number of possible genotypes given ploidy and the maximum allele index.
     * @return never {@code null}.
     */
    public int genotypeCount()  {
        return genotypeCount;
    }

    /**
     * Returns the genotype associated to a particular likelihood index.
     *
     * <p>If {@code index} is larger than {@link GenotypeLikelihoodCalculators#MAXIMUM_STRONG_REF_GENOTYPE_PER_PLOIDY},
     *  this method will reconstruct that genotype-allele-count iteratively from the largest strongly referenced count available.
     *  or the last requested index genotype.
     *  </p>
     *
     * <p> Therefore if you are iterating through all genotype-allele-counts you should do sequentially and incrementally, to
     * avoid a large efficiency drop </p>.
     *
     * @param index query likelihood-index.
     * @return never {@code null}.
     */
    public GenotypeAlleleCounts genotypeAlleleCountsAt(final int index) {
        if (index < 0 || index >= genotypeCount)
            throw new IllegalArgumentException("invalid likelihood index: " + index + " >= " + genotypeCount
                    + " (genotype count for nalleles = " + alleleCount + " and ploidy " + ploidy );
        if (index < GenotypeLikelihoodCalculators.MAXIMUM_STRONG_REF_GENOTYPE_PER_PLOIDY)
            return genotypeAlleleCounts[index];
        else if (lastOverheadCounts == null || lastOverheadCounts.index() > index) {
            final GenotypeAlleleCounts result = genotypeAlleleCounts[GenotypeLikelihoodCalculators.MAXIMUM_STRONG_REF_GENOTYPE_PER_PLOIDY - 1].clone();
            result.increase(index - GenotypeLikelihoodCalculators.MAXIMUM_STRONG_REF_GENOTYPE_PER_PLOIDY + 1);
            lastOverheadCounts = result;
            return result.clone();
        } else {
            lastOverheadCounts.increase(index - lastOverheadCounts.index());
            return lastOverheadCounts.clone();
        }
    }

    /**
     * Calculate the likelihoods given the list of alleles and the likelihood map.
     *
     * <p>This operation is <b>thread-unsafe</b>.</p>
     *
     * @param likelihoods the likelihood matrix all alleles vs all reads.
     *
     * @throws IllegalArgumentException if {@code alleleList} is {@code null} or {@code likelihoods} is {@code null}
     *     or the alleleList size does not match the allele-count of this calculator, or there are missing allele vs
     *     read combinations in {@code likelihoods}.
     *
     * @return never {@code null}.
     */
    public <A extends Allele> GenotypeLikelihoods genotypeLikelihoods(final ReadLikelihoods.Matrix<A> likelihoods) {
        if (likelihoods == null)
            throw new IllegalArgumentException("the likelihood map cannot be null");

        if (likelihoods.alleleCount() != alleleCount)
            throw new IllegalArgumentException("mismatch between allele list and alleleCount");


        final int readCount = likelihoods.readCount();


        ensureReadCapacity(readCount);

        /// [x][y][z] = z * LnLk(Read_x | Allele_y)
        final double[] readLikelihoodComponentsByAlleleCount
                = readLikelihoodComponentsByAlleleCount(likelihoods);
        final double[][] genotypeLikelihoodByRead = genotypeLikelihoodByRead(readLikelihoodComponentsByAlleleCount,readCount);
        final double[] readLikelihoodsByGenotypeIndex = genotypeLikelihoods(genotypeLikelihoodByRead, readCount);
        return GenotypeLikelihoods.fromLog10Likelihoods(readLikelihoodsByGenotypeIndex);
    }

    /**
     * Calculates the final genotype likelihood array out of the likelihoods for each genotype per read.
     *
     * @param readLikelihoodsByGenotypeIndex <i>[g][r]</i> likelihoods for each genotype <i>g</i> and <i>r</i>.
     * @param readCount number of reads in the input likelihood arrays in {@code genotypeLikelihoodByRead}.
     * @return never {@code null}, one position per genotype where the <i>i</i> entry is the likelihood of the ith
     *   genotype (0-based).
     */
    private double[] genotypeLikelihoods(final double[][] readLikelihoodsByGenotypeIndex, final int readCount) {
        final double[] result = new double[genotypeCount];
        final double denominator = readCount * log10[ploidy]; // instead of dividing each read likelihood by ploidy
         // ( so subtract log10(ploidy) )  we multiply them all and the divide by ploidy^readCount (so substract readCount * log10(ploidy) )
        for (int g = 0; g < genotypeCount; g++) {
            final double[] likelihoodsByRead = readLikelihoodsByGenotypeIndex[g];
            double s = - denominator;
            for (int r = 0; r < readCount; r++)
                s += likelihoodsByRead[r];
            result[g] = s;
        }
        return result;
    }

    /**
     * Calculates the likelihood component of each read on each genotype.
     *
     * @param readLikelihoodComponentsByAlleleCount [a][f][r] likelihood stratified by allele <i>a</i>, frequency in genotype <i>f</i> and
     *                                              read <i>r</i>.
     * @param readCount number of reads in {@code readLikelihoodComponentsByAlleleCount}.
     * @return never {@code null}.
     */
    private double[][] genotypeLikelihoodByRead(final double[] readLikelihoodComponentsByAlleleCount, final int readCount) {

        // Here we don't use the convenience of {@link #genotypeAlleleCountsAt(int)} within the loop to spare instantiations of
        // GenotypeAlleleCounts class when we are dealing with many genotypes.
        GenotypeAlleleCounts alleleCounts = genotypeAlleleCounts[0];

        for (int genotypeIndex = 0; genotypeIndex < genotypeCount; genotypeIndex++) {
            final double[] readLikelihoods = this.readLikelihoodsByGenotypeIndex[genotypeIndex];
            final int componentCount = alleleCounts.distinctAlleleCount();
            switch (componentCount) {
                case 1: //
                    singleComponentGenotypeLikelihoodByRead(alleleCounts, readLikelihoods, readLikelihoodComponentsByAlleleCount, readCount);
                    break;
                case 2:
                    twoComponentGenotypeLikelihoodByRead(alleleCounts,readLikelihoods,readLikelihoodComponentsByAlleleCount, readCount);
                    break;
                default:
                    manyComponentGenotypeLikelihoodByRead(alleleCounts,readLikelihoods,readLikelihoodComponentsByAlleleCount, readCount);
            }
            if (genotypeIndex < genotypeCount - 1)
                alleleCounts = nextGenotypeAlleleCounts(alleleCounts);
        }
        return readLikelihoodsByGenotypeIndex;
    }

    private GenotypeAlleleCounts nextGenotypeAlleleCounts(final GenotypeAlleleCounts alleleCounts) {
        final int index = alleleCounts.index();
        final GenotypeAlleleCounts result;
        final int cmp = index - GenotypeLikelihoodCalculators.MAXIMUM_STRONG_REF_GENOTYPE_PER_PLOIDY + 1;
        if (cmp < 0)
            result = genotypeAlleleCounts[index + 1];
        else if (cmp == 0) {
            result = genotypeAlleleCounts[index].clone();
            result.increase();
        } else {
            alleleCounts.increase();
            result = alleleCounts;
        }
        return result;
    }

    /**
     * General genotype likelihood component by thread calculator. It does not make any assumption in the exact
     * number of alleles present in the genotype.
     */
    private void manyComponentGenotypeLikelihoodByRead(final GenotypeAlleleCounts genotypeAlleleCounts,
                                                       final double[] likelihoodByRead,
                                                       final double[]readLikelihoodComponentsByAlleleCount,
                                                       final int readCount) {

        // First we collect the allele likelihood component for all reads and place it
        // in readGenotypeLikelihoodComponents for the final calculation per read.
        genotypeAlleleCounts.copyAlleleCounts(genotypeAllelesAndCounts,0);
        final int componentCount = genotypeAlleleCounts.distinctAlleleCount();
        final int alleleDataSize = (ploidy + 1) * readCount;
        for (int c = 0,cc = 0; c < componentCount; c++) {
            final int alleleIndex = genotypeAllelesAndCounts[cc++];
            final int alleleCount = genotypeAllelesAndCounts[cc++];
            // alleleDataOffset will point to the index of the first read likelihood for that allele and allele count.
            int alleleDataOffset = alleleDataSize * alleleIndex + alleleCount * readCount;
            for (int r = 0, readDataOffset = c; r < readCount; r++, readDataOffset += maximumDistinctAllelesInGenotype)
                readGenotypeLikelihoodComponents[readDataOffset] = readLikelihoodComponentsByAlleleCount[alleleDataOffset++];
        }

        // Calculate the likelihood per read.
        for (int r = 0, readDataOffset = 0; r < readCount; r++, readDataOffset += maximumDistinctAllelesInGenotype)
            likelihoodByRead[r] = MathUtils.approximateLog10SumLog10(readGenotypeLikelihoodComponents, readDataOffset, readDataOffset + componentCount);
    }

    /**
     * Calculates the likelihood component by read for a given genotype allele count assuming that there are
     * exactly two alleles present in the genotype (with arbitrary non-zero counts each).
     */
    private void twoComponentGenotypeLikelihoodByRead(final GenotypeAlleleCounts genotypeAlleleCounts,
                                                      final double[] likelihoodByRead,
                                                      final double[] readLikelihoodComponentsByAlleleCount,
                                                      final int readCount) {
        final int allele0 = genotypeAlleleCounts.alleleIndexAt(0);
        final int freq0 = genotypeAlleleCounts.alleleCountAt(0);
        final int allele1 = genotypeAlleleCounts.alleleIndexAt(1);
        final int freq1 = ploidy - freq0; // no need to get it from genotypeAlleleCounts.
        int allele0LnLkOffset = readCount * ((ploidy + 1) * allele0 + freq0);
        int allele1LnLkOffset = readCount * ((ploidy + 1) * allele1 + freq1);
        for (int r = 0; r < readCount; r++) {
            final double lnLk0 = readLikelihoodComponentsByAlleleCount[allele0LnLkOffset++];
            final double lnLk1 = readLikelihoodComponentsByAlleleCount[allele1LnLkOffset++];
            likelihoodByRead[r] = MathUtils.approximateLog10SumLog10(lnLk0,lnLk1);
        }
    }

    /**
     * Calculates the likelihood component by read for a given genotype allele count assuming that there are
     * exactly one allele present in the genotype.
     */
    private void singleComponentGenotypeLikelihoodByRead(final GenotypeAlleleCounts genotypeAlleleCounts,
                                                         final double[] likelihoodByRead, final double[] readLikelihoodComponentsByAlleleCount, final int readCount) {
        final int allele = genotypeAlleleCounts.alleleIndexAt(0);
        // the count of the only component must be = ploidy.
        int offset = (allele * (ploidy + 1) + ploidy) * readCount;
        for (int r = 0; r < readCount; r++)
            likelihoodByRead[r] =
                    readLikelihoodComponentsByAlleleCount[offset++];
    }

    /**
     * Returns a 3rd matrix with the likelihood components.
     *
     * <pre>
     *     result[y][z][x] :=  z * lnLk ( read_x | allele_y ).
     * </pre>
     *
     * @return never {@code null}.
     */
    private <A extends Allele> double[] readLikelihoodComponentsByAlleleCount(final ReadLikelihoods.Matrix<A> likelihoods) {
        final int readCount = likelihoods.readCount();
        final int alleleDataSize = readCount * (ploidy + 1);

        // frequency1Offset = readCount to skip the useless frequency == 0. So now we are at the start frequency == 1
        // frequency1Offset += alleleDataSize to skip to the next allele index data location (+ readCount) at each iteration.
        for (int a = 0, frequency1Offset = readCount; a < alleleCount; a++, frequency1Offset += alleleDataSize) {
            likelihoods.copyAlleleLikelihoods(a, readAlleleLikelihoodByAlleleCount, frequency1Offset);

            // p = 2 because the frequency == 1 we already have it.
            for (int frequency = 2, destinationOffset = frequency1Offset + readCount; frequency <= ploidy; frequency++) {
                final double log10frequency = log10[frequency];
                for (int r = 0, sourceOffset = frequency1Offset; r < readCount; r++)
                    readAlleleLikelihoodByAlleleCount[destinationOffset++] =
                            readAlleleLikelihoodByAlleleCount[sourceOffset++] + log10frequency;
            }
        }
        return readAlleleLikelihoodByAlleleCount;
    }

    /**
     * Returns the ploidy for this genotype likelihood calculator.
     * @return 0 or greater.
     */
    public int ploidy() {
        return ploidy;
    }

    /**
     * Returns the total number of alleles for this genotype calculator.
     * @return the number of alleles considered by this calculator.
     */
    public int alleleCount() {
        return alleleCount;
    }

    /**
     * Returns the likelihood index given the allele counts.
     *
     * @param alleleCountArray the query allele counts. This must follow the format returned by
     *  {@link GenotypeAlleleCounts#copyAlleleCounts} with 0 offset.
     *
     * @throws IllegalArgumentException if {@code alleleCountArray} is not a valid {@code allele count array}:
     *  <ul>
     *      <li>is {@code null},</li>
     *      <li>or its length is not even,</li>
     *      <li>or it contains any negatives,
     *      <li>or the count sum does not match the calculator ploidy,</li>
     *      <li>or any of the alleles therein is negative or greater than the maximum allele index.</li>
     *  </ul>
     *
     * @return 0 or greater but less than {@link #genotypeCount}.
     */
    public int alleleCountsToIndex(final int ... alleleCountArray) {
        if (alleleCountArray == null)
            throw new IllegalArgumentException("the allele counts cannot be null");
        if ((alleleCountArray.length & 1) != 0)
            throw new IllegalArgumentException("the allele counts array cannot have odd length");
        alleleHeap.clear();
        for (int i = 0; i < alleleCountArray.length; i += 2) {
            final int index = alleleCountArray[i];
            final int count = alleleCountArray[i+1];
            if (count < 0)
                throw new IllegalArgumentException("no allele count can be less than 0");
            for (int j = 0; j < count; j++)
                alleleHeap.add(index);
        }
        return alleleHeapToIndex();
    }

    /**
     * Transforms the content of the heap into an index.
     *
     * <p>
     *     The heap contents are flushed as a result, so is left ready for another use.
     * </p>
     *
     * @return a valid likelihood index.
     */
    private int alleleHeapToIndex() {
        if (alleleHeap.size() != ploidy)
            throw new IllegalArgumentException("the sum of allele counts must be equal to the ploidy of the calculator");
        if (alleleHeap.peek() >= alleleCount)
            throw new IllegalArgumentException("invalid allele " + alleleHeap.peek() + " more than the maximum " + (alleleCount - 1));
        int result = 0;
        for (int p = ploidy; p > 0; p--) {
            final int allele = alleleHeap.remove();
            if (allele < 0)
                throw new IllegalArgumentException("invalid allele " + allele + " must be equal or greater than 0 ");
            result += alleleFirstGenotypeOffsetByPloidy[p][allele];
        }
        return result;
    }

    /**
     * Composes a genotype index map given a allele index recoding.
     *
     * @param oldToNewAlleleIndexMap allele recoding. The ith entry indicates the index of the allele in original encoding
     *                               that corresponds to the ith allele index in the final encoding.
     *
     * @throws IllegalArgumentException if this calculator cannot handle the recoding provided. This is
     * the case when either {@code oldToNewAlleleIndexMap}'s length or any of its element (+ 1 as they are 0-based) is larger
     * this calculator's {@link #alleleCount()}. Also if any {@code oldToNewAllelesIndexMap} element is negative.
     *
     * @return never {@code null}.
     */
    public int[] genotypeIndexMap(final int[] oldToNewAlleleIndexMap) {
        if (oldToNewAlleleIndexMap == null)
            throw new IllegalArgumentException("the input encoding array cannot be null");

        final int resultAlleleCount = oldToNewAlleleIndexMap.length;
        if (resultAlleleCount > alleleCount)
            throw new IllegalArgumentException("this calculator does not have enough capacity for handling "
                    + resultAlleleCount + " alleles ");
        final int resultLength = resultAlleleCount == alleleCount
                ? genotypeCount : GenotypeLikelihoodCalculators.genotypeCount(ploidy,resultAlleleCount);

        final int[] result = new int[resultLength];
        final int[] sortedAlleleCounts = new int[Math.max(ploidy,alleleCount) << 1];
        alleleHeap.clear();
        GenotypeAlleleCounts alleleCounts = genotypeAlleleCounts[0];
        for (int i = 0; i < resultLength; i++) {
            genotypeIndexMapPerGenotypeIndex(i,alleleCounts, oldToNewAlleleIndexMap, result, sortedAlleleCounts);
            if (i < resultLength - 1)
                  alleleCounts = nextGenotypeAlleleCounts(alleleCounts);
        }
        return result;
    }

    /**
     * Performs the genotype mapping per new genotype index.
     *
     * @param newGenotypeIndex the target new genotype index.
     * @param alleleCounts tha correspond to {@code newGenotypeIndex}.
     * @param oldToNewAlleleIndexMap the allele mapping.
     * @param destination where to store the new genotype index mapping to old.
     * @param sortedAlleleCountsBuffer a buffer to re-use to get the genotype-allele-count's sorted allele counts.
     */
    private void genotypeIndexMapPerGenotypeIndex(final int newGenotypeIndex, final GenotypeAlleleCounts alleleCounts, final int[] oldToNewAlleleIndexMap, final int[] destination, final int[] sortedAlleleCountsBuffer) {
        final int distinctAlleleCount = alleleCounts.distinctAlleleCount();
        alleleCounts.copyAlleleCounts(sortedAlleleCountsBuffer,0);
        for (int j = 0, jj = 0; j < distinctAlleleCount; j++) {
            final int oldIndex = sortedAlleleCountsBuffer[jj++];
            final int repeats = sortedAlleleCountsBuffer[jj++];
            final int newIndex = oldToNewAlleleIndexMap[oldIndex];
            if (newIndex < 0 || newIndex >= alleleCount)
                throw new IllegalArgumentException("found invalid new allele index (" + newIndex + ") for old index (" + oldIndex + ")");
            for (int k = 0; k < repeats; k++)
                alleleHeap.add(newIndex);
        }
        final int genotypeIndex = alleleHeapToIndex(); // this cleans the heap for the next use.
        destination[newGenotypeIndex] = genotypeIndex;
    }

}
