Package main

Interface Summary

Interface	Description
GenotypeValues	Interface GenotypeValues represents a value for each possible genotype for each sample at each marker.

Class Summary

Class	Description
CurrentData	Class CurrentData represents input data for the current marker window.
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.
Par	Class Parameters represents the parameters for a Beagle analysis.
Pedigree	Class Pedigree stores parent-offspring relationships in a list of samples.
RunStats	Class RunStats contains methods for storing and printing statistics describing a Beagle analysis.
WindowWriter	Class WindowWriter writes VCF and IBD output data.