/**
* Returns a list of {@code this.nCopies()} sampled haplotype pairs for the specified parent
* ({@code sampleA}) and offspring ({@code sampleB}). Haplotype pairs are sampled conditional on
* the HMM with transition probabilities determined by {@code this.dag()} and emission
* probabilities determined by {@code this.gl()}. Posterior genotype probabilities for the parent
* and offspring are written to {@code gtProbsA} and {@code gtProbsB} respectively. The posterior
* probability of the {@code j}-th genotype for the {@code k}-th marker is stored at index {@code
* gl.markers().sumGenotypes(k) + j} in the {@code gtProbsA} and {@code gtProbsB} arrays. The
* contract for this method is unspecified if no parent haplotype pairs or no offspring haplotype
* pairs are consistent with the HMM.
*
* @param sampleA the sample index of the parent.
* @param sampleB the sample index of the offspring.
* @param gtProbsA an array to which posterior genotype probabilities for the parent will be
* written.
* @param gtProbsB an array to which posterior genotype probabilities for the offspring will be
* written.
* @return a list of {@code this.nCopies()} sampled haplotype pairs for the specified individuals.
* @throws IndexOutOfBoundsException if {@code sampleA<0 || sampleA>=this.gl().nSamples()}
* @throws IndexOutOfBoundsException if {@code sampleB<0 || sampleB>=this.gl().nSamples()}
* @throws IllegalArgumentException if {@code gtProbsA.length!=this.gl().markers().sumGenotypes()}
* @throws IllegalArgumentException if {@code gtProbsB.length!=this.gl().markers().sumGenotypes()}
* @throws NullPointerException if {@code gtProbsA==null || gtProbsB==null}
*/
public List<HapPair> sample(int sampleA, int sampleB, double[] gtProbsA, double[] gtProbsB) {
checkGprobs(gtProbsA, gtProbsB);
forwardAlgorithm(sampleA, sampleB);
initSampleAlleles(currentLevel(), sampleA, sampleB);
currentLevel().setInitialBackwardValues(bwdNodes);
setGprobs(currentLevel(), gtProbsA, gtProbsB);
for (int j = nMarkers - 2; j >= 0; --j) {
DuoBaumLevel level = previousLevel(sampleA, sampleB);
sampleAlleles(level, sampleA, sampleB);
level.setBackwardValues(bwdNodes);
setGprobs(level, gtProbsA, gtProbsB);
}
return hapList(sampleA, sampleB);
}
