Package imp

Interface Summary

Interface	Description
StateProbs	Class StateProbs stores a subset of Li and Stephens HMM states and associated probabilities for a target haplotype.

Class Summary

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