AlleleImputer |
Class AlleleImputer imputes alleles from marker allele
frequencies.
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BestMatch |
Class BestMatch has methods for finding a haplotype
that shares a long IBS sequence containing a specified genomic interval
with a target haplotype and that originates from a sample which
carries a rare variant in the specified genomic interval
that is also carried by the target sample.
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CodedSteps |
Class CodedSteps divides phased genotype data
into non-overlapping intervals (the steps), indexes the unique
allele sequences in each interval, and stores a map of haplotype
index to allele sequence index for each interval.
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EstPhase |
Class EstPhase stores original input genotype data.
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FixedPhaseData |
Class FixedPhaseData stores immutable data for a
marker window.
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FwdBwd |
Class FwdBwd implements computes HMM reference haplotypes
and state probabilities.
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HapImputer |
Class ImputableHaps performs imputation to estimate
missing alleles and missing haplotype phase.
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HmmUpdater |
Instances of class HmmUpdater have methods for one-step
updates of forward or backward HMM values.
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Ibs2 |
Class Ibs2 stores IBS2 segments that any target sample shares
with another target or reference sample.
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ImputeBaum |
Class ImputeBaum applies the forward and backward algorithms
for a haploid Li and Stephens hidden Markov model at high-frequency markers,
and imputes missing genotypes and heterozygote phase at low-frequency
markers.
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LowFreqPhaseIbs |
Class LowFreqPhaseIbs identifies haplotypes that share a long
IBS segment or a low frequency variant with a specified haplotype
in a specified genomic interval.
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PbwtPhaseIbs |
Class PbwtPhaseIBS uses the Positional Burrows-Wheeler
Transform (PBWT) to find long IBS haplotypes for each sample that
contain a specified small genomic interval.
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PhaseBaum1 |
Class PhaseBaum1 implements the forward and backward algorithms
for a haploid Li and Stephens hidden Markov model.
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PhaseData |
Class PhaseData contains the current input data for updating
genotype phase.
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PhaseLS |
Class PhaseLS estimated genotypes phase using
a haploid Li and Stephens hidden Markov model.
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PhaseStates |
Class PhaseStates has methods for constructing a Li and
Stephens HMM for a target haplotype or target sample.
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RecombRegress |
Class RecombRegress uses linear regression to estimate the
recombination factor for a haploid Li and Stephens hidden Markov model.
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SampleSeg |
Class SampleSeg represents a haplotype shared with a sample.
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