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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 <valentin@broadinstitute.org>
*/
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;
}
}