| 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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| HaplotypeCoder |
Class HaplotypeCoder indexes the observed allele sequences
in phased reference and target genotype data in a chromosome interval.
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| ImpData |
Class ImpData contains the input data for imputation of
ungenotyped markers.
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| ImpIbs |
Class ImpIbs identifies haplotypes that share a long
IBS segment with a specified haplotype.
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| ImpLS |
Class ImpLS computes HMM state probabilities
at genotyped markers in the target haplotypes.
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| ImpLSBaum |
Class ImpLSBaum implements a Baum hidden Markov model
forward and backward algorithms for computing HMM state probabilities
at genotyped markers using IBS-matched reference haplotypes.
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| ImpStates |
Class ImpStates identifies a list of pseudo-reference haplotypes
for a target haplotype.
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| ImputedRecBuilder |
Class ImputeRecBuilder contains methods for constructing
and printing a VCF record in VCF 4.3 format.
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| ImputedVcfWriter |
Class ImputedVcfWriter writes observed and imputed genotypes
to a VCF output file.
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| RefHapHash |
Class RefHapHash stores a hash code for each haplotype
in a sublist of reference haplotypes.
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| StateProbsFactory |
Class StateProbsFactory stores HMM state probabilities
that that can be used to imputed impute missing HMM state probabilities
using linear interpolation.
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