public interface SingleBaumInterface
Interface SingleBaumInterface
has methods for sampling
haplotype pairs.
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.
|
Dag dag()
GL gl()
int nSamplesPerIndividual()
long seed()
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.
sample
- a sample indexthis.nSamplesPerIndividual()
sampled
haplotype pairs for the specified individualjava.lang.IndexOutOfBoundsException
- if
sample < 0 || sample >= this.gl().nSamples()
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.
sample
- the sample indexgtProbs
- a array to which posterior genotype probabilities
for the sample will be writtenthis.nSamplesPerIndividual()
sampled
haplotype pairs for the specified individualjava.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