Interface | Description |
---|---|
DiploidStates |
Class
DiploidStates represents a list of iterators
(one iterator for each marker) that iterate over a subset of diploid
HMM states at a marker. |
SingleBaumInterface |
Interface
SingleBaumInterface has methods for sampling
haplotype pairs. |
Class | Description |
---|---|
ConsumeSingleSamples |
Class
ConsumeSingleSamples samples haplotype pairs conditional
on the observed genotype data and a haplotype frequency model. |
DuoBaumLevel |
Class
DuoBaumLevel computes forward and backward Baum
values at a level of a hidden Markov model (HMM) whose states are
ordered edge trios of a leveled directed acyclic graph (DAG). |
DuoNodes |
Class
DuoNodes stores ordered node trios and associated values. |
HapBaumLevel |
Class
HapBaumLevel computes forward and backward Baum values for a
haploid hidden Markov model (HMM) whose states are edges of a leveled
directed acyclic graph (DAG). |
HaplotypeCoder |
Class
HaplotypeCoder indexes the observed allele sequences
in reference and target haplotype pairs for a list of consecutive markers. |
HapNodes |
Class
HapNodes stores nodes and associated values. |
ImputationData |
Class
ImputationData contains the input data that is
required for imputation of ungenotyped markers in the imputation target. |
LSHapBaum |
Class
LSHapBaum implements the Baum hidden Markov model
forward and backward algorithms for imputing missing alleles on a
target haplotype. |
RecombSingleBaum |
Class
RestrictedSingleBaum implements the Baum forward and
backward algorithms for a hidden Markov model (HMM) of an individual's
genotype data. |
RecombSingleBaumLevel |
Class
RestrictedSingleBaumLevel computes forward and backward
Baum values at a level of a hidden Markov model (HMM) whose states are
ordered edge pairs of a leveled directed acyclic graph (DAG). |
RecombSingleNodes |
Class
RecombSingleNodes stores ordered node pairs and
associated values. |
RefHapSeg |
Class
RefHapSeg represents a chromosome segment of
reference haplotypes. |
RefHapSegs |
Class
RefHapSegs represents reference haplotypes that span
segments determined by non-overlapping clusters of markers. |
RestrictedDag |
Class
RestrictedDag is a wrapper for a Dag
object that stores segments of identity by descent. |
SamplerData |
Class
SamplerData contains immutable input data for the
current marker window. |
SingleBaum |
Class
SingleBaum implements the Baum forward and backward
algorithms for a hidden Markov model (HMM) of an individual's genotype data. |
SingleBaumLevel |
Class
SingleBaumLevel computes forward and backward Baum
values at a level of a hidden Markov model (HMM) whose states are
ordered edge pairs of a leveled directed acyclic graph (DAG). |
SingleNodes |
Class
SingleNodes stores ordered node pairs and associated values. |