sample

Interface SingleBaumInterface

All Known Implementing Classes:

RecombSingleBaum, SingleBaum

public interface SingleBaumInterface

Interface SingleBaumInterface has methods for sampling haplotype pairs.

Method Summary

Modifier and Type	Method and Description
Dag	dag() Returns the directed acyclic graph that determines the transition probabilities.
GL	gl() Returns the emission probabilities.
int	nSamplesPerIndividual() Returns the number of haplotype pairs that are sampled for each individual.
java.util.List<HapPair>	randomSample(int sample) Returns a list of this.nSamplesPerIndividual() sampled haplotype pairs for the specified individual.
java.util.List<HapPair>	randomSample(int sample, double[] gtProbs) Returns a list of this.nSamplesPerIndividual() sampled haplotype pairs for the specified individual.
long	seed() Returns the initial random seed.

Method Detail

dag

Dag dag()

Returns the directed acyclic graph that determines the transition probabilities.

Returns:

the directed acyclic graph that determines the transition probabilities

gl

GL gl()

Returns the emission probabilities.

Returns:

the emission probabilities

nSamplesPerIndividual

int nSamplesPerIndividual()

Returns the number of haplotype pairs that are sampled for each individual.

Returns:

the number of haplotype pairs that are sampled for each individual

seed

long seed()

Returns the initial random seed.

Returns:

the initial random seed

randomSample

java.util.List<HapPair> randomSample(int sample)

Returns a list of this.nSamplesPerIndividual() sampled haplotype pairs for the specified individual. Haplotype pairs are sampled conditional on the HMM with transition probabilities determined by this.dag() and emission probabilities determined by this.gl().

The contract for this method is unspecified if no haplotype pair is consistent with the HMM.

Parameters:

sample - a sample index

Returns:

a list of this.nSamplesPerIndividual() sampled haplotype pairs for the specified individual

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.gl().nSamples()

randomSample

java.util.List<HapPair> randomSample(int sample,
                                     double[] gtProbs)

Returns a list of this.nSamplesPerIndividual() sampled haplotype pairs for the specified individual. Haplotype pairs are sampled conditional on the HMM with transition probabilities determined by this.dag() and emission probabilities determined by this.gl(). Posterior genotype probabilities are written to the specified array. The posterior probability of the j-th genotype for the k-th marker is stored at index gl.markers().sumGenotypes(k) + j in the gtProbs array.

The contract for this method is unspecified if no haplotype pair is consistent with the HMM.

Parameters:

sample - the sample index

gtProbs - a array to which posterior genotype probabilities for the sample will be written

Returns:

a list of this.nSamplesPerIndividual() sampled haplotype pairs for the specified individual

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.gl().nSamples()

java.lang.IllegalArgumentException - if gtProbs.length != this.gl().markers().sumGenotypes()

java.lang.NullPointerException - if gtProbs == null