| BasicPhaseStates |
Class BasicPhaseStates has methods for constructing a Li and
Stephens HMM for a target haplotype or 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 input genotype data and the
current estimated phased genotypes for each target sample.
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| FixedPhaseData |
Class FixedPhaseData stores immutable data for a
marker window.
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| FwdPbwtPhaser |
Class FwdPbwtPhaser phases input genotype data and imputes
missing alleles using the Positional Burrows-Wheeler Transform (PBWT).
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| HmmParamData |
Class HmmParamData generates data for estimating
allele mismatch and recombination intensity parameters for a
haploid Li and Stephens hidden Markov model.
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| HmmStateProbs |
Class HmmStateProbs has a method that returns the reference
haplotype and probability associated with each HMM state.
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| HmmUpdater |
Class HmmUpdater has static methods for next marker
updates of forward and backward HMM values.
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| Ibs2 |
Class Ibs2 stores IBS2 segments that any target sample shares
with another target sample.
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| Ibs2Markers |
Class Ibs2Markers stores the markers and intervals that are
used to detect IBS2 segments.
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| Ibs2Sets |
Class Ibs2Sets partitions markers into steps, and stores
the sets of samples whose genotypes are consistent with IBS2 in each
step.
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| LowFreqPbwtPhaseIbs |
Class AltPbwtPhaseIBS uses the Positional Burrows-Wheeler
Transform (PBWT) and rare variants to select IBS haplotypes for each
sample for each specified genomic interval.
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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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| LowFreqPhaseStates |
Class LowFreqPhaseStates has methods for constructing a Li and
Stephens HMM for a target haplotype.
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| MarkerCluster |
Class MarkerCluster represents a partition of markers into
contiguous marker clusters.
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| ParamEstimates |
Class ParamEstimates estimates the allele mismatch probability
and the recombination intensity for a haploid Li and Stephens hidden
Markov model.
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| PbwtIbsData |
Class PbwtIbsData contains parameters and data for finding
haplotypes that share an IBS segment with a target haplotype.
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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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| PbwtPhaser |
Class PbwtPhaser phases input genotype data and imputes
missing alleles using the Positional Burrows-Wheeler Transform (PBWT)
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| PbwtRecPhaser |
Class PbwtRecPhaser partially phases and imputes genotypes
using the Positional Burrows-Wheeler transform.
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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 stores the current genotype phase estimates
and parameter values.
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| PhaseLS |
Class PhaseLS contains static methods for estimated genotypes
phase using a haploid Li and Stephens hidden Markov model.
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| RevPbwtPhaser |
Class RevPbwtPhaser phases input genotype data and imputes
missing alleles using the Positional Burrows-Wheeler Transform (PBWT).
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| SamplePhase |
Each instance of class SamplePhase stores an estimated haplotype
pair for a sample, the list of markers with missing genotypes for the sample,
a list of markers whose genotype phase with respect to the preceding
heterozygote genotype is considered to be uncertain for the sample, and
a set of marker clusters for the sample.
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| SampleSeg |
Class SampleSeg represents a segment of genotype data in
a sample.
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| Stage2Baum |
Class Stage2Baum 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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| Stage2Haps |
Class Stage2Haps stores phased genotypes.
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