Package main

Interface Summary

Interface	Description
AlleleProbs	Interface AlleleProbs represents per-haplotype allele probabilities for a list of samples.
GeneticMap	Interface GeneticMap represents a genetic map for one or more chromosomes.
GenotypeValues	Interface GenotypeValues represents a value for each possible genotype for each sample at each marker.
HapAlleleProbs	Interface HapAlleleProbs stores allele probabilities for a haplotype.

Class Summary

Class	Description
BasicAlleleProbs	Class BasicAlleleProbs stores per-haplotype allele probabilities for a list of samples.
BasicGenotypeValues	Class BasicGenotypeValues stores values for each possible genotype for each sample at each marker.
ConstrainedAlleleProbs	Class ConstrainedAlleleProbs is a wrapper for an AlleleProbs instance that changes the wrapped haplotype allele probabilities for a subset of markers.
CurrentData	Class CurrentData represents input data for the current marker window.
HapPairSampler	Class HapPairSampler samples haplotype pairs and estimates posterior genotype probabilities.
LiAndStephensHapSampler	Class LiAndStephensHapSampler estimates posterior allele probabilities.
LowMemHapAlleleProbs	Class LowMemHapAlleleProbs stores allele probabilities for a haplotype.
Main	Class Main is the entry class for the Beagle program.
MainHelper	Class MainHelper is an auxiliary class with methods called by the main.Main class.
NuclearFamilies	Class NuclearFamilies stores parent-offspring relationships in a list of samples.
Par	Class Parameters represents the parameters for a Beagle analysis.
PlinkGeneticMap	Class PlinkGeneticMap represents a genetic map derived from a PLINK map file with map positions in cM units for one or more chromosomes.
PositionMap	Class PositionMap represents a genetic map obtained by multiplying chromosome position by a scale factor.
RecombHapPairSampler	Class RecombHapPairSamples samples haplotype pairs and estimates posterior genotype probabilities using a haplotype frequency model that permits transitions between any two states at adjacent markers.
RevGenotypeValues	Class RevGenotypeValues is a wrapper for a GenotypeValues instance.
RunStats	Class RunStats contains methods for storing and printing statistics describing a Beagle analysis.
SampleGenotypeValues	Class SampleGenotypeValues stores a value for each possible genotype at each marker for one sample.
SampleHapPairAlleleProbs	Class SampleHapPairAlleleProbs is a wrapper for a SampleHapPairs instance.
WindowWriter	Class WindowWriter writes VCF and IBD output data.