All Classes

Class	Description
AllData	Class AllData represents a sliding window of reference and target VCF recList.
AsIsBref3Writer	Class AsIsBref3Writer writes VCF data with phased, non-missing genotypes to a binary reference format v3 (bref) file.
BasicGT	Class BasicGT represents genotype emission probabilities for a set of samples.
BasicMarker	Class BasicMarker represents a genetic marker.
BasicRefGT	Class BasicRefGT stores a list of samples and a haplotype pair for each sample.
BGZIPOutputStream	Class BGZIPOutputStream is an output stream filter that performs BGZIP compression.
BitHapPair	Class BitHapPair represents a pair of haplotypes for a sample.
BitSetGT	Class BitSetGT represents genotype emission probabilities for a list of samples at a single marker.
Bref3	Class Bref3 converts files in VCF format into bref version 3 format.
Bref3It	Class Bref3It represents an iterator whose next() which returns records from a bref version 3 file.
Bref3Reader	Class Bref3Reader contains methods for reading a bref 3 (binary reference format) file.
BrefBlock	Class BrefBlock represents starting chromosome coordinates and file offset for the start of a binary reference format (bref) data block.
BrefWriter	Interface BrefWrites writes phased, non-missing genotypes to a binary reference format (bref) file.
CharArray	/**
ChromIds	Class ChromIds is a singleton class that represents a list of chromosome identifiers.
ChromInterval	Class ChromInterval represents a chromosome interval whose end points are genome coordinates.
CompressBref3Writer	Class CompressBref3Writer writes phased, non-missing genotypes to a binary reference format v3 (bref) file.
Const	Class Const provides public static final fields with string and character constants.
CurrentData	Class CurrentData represents input data for the current marker window.
Data	Interface Data represents a sliding window of target VCF records or a sliding window of reference and target VCF records.
DuplicatesGTRec	Interface DuplicatesGTRec represents marker alleles for a list of samples.
EstPhase	Class EstPhase stores haplotype pairs, missing genotypes, and unphased, nonmissing heteroygote genotypes for a list of samples.
FileIt<E>	An iterator for data elements in a file.
FileUtil	Class FileUtil contains static methods for working with files.
Filter<E>	A filter for accepting or rejecting objects.
FilterUtil	Class FilterUtil contains static methods for constructing marker filters.
FloatArray	Class FloatArray represents an immutable list of float floating point values.
FloatList	Class FloatList represents a list of floats.
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.
GT	Interface GT represents genotype data for a list of markers and a list of samples.
GTRec	Interface GTRec represents represents genotype data for one marker.
HaplotypeCoder	Class HaplotypeCoder indexes the observed allele sequences in phased reference and target genotype data in a chromosome interval.
HapPair	Interface HapPair represents a pair of haplotypes for a sample.
HapPairPhasedGT	Class HapPairPhasedGT stores a list of samples and a haplotype pair for each sample.
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.
IndexArray	Class IndexArray stores an array whose entries are elements of a bounded set of non-negative integers along with an upper bound.
InitTargHapPairs	Class InitTargHapPairs has a static method for returning initial target haplotype pairs.
InputIt	Class InputIt is a buffered iterator whose next() method returns lines of a text input stream.
IntArray	Interface IntArray represents an immutable int[] array.
IntervalVcfIt<E extends MarkerContainer>	Class IntervalVcfIterator is a sample file iterator whose next() method returns a marker container.
IntInterval	Interface IntInterval represents an interval of consecutive integers.
IntList	Class IntList represents a list of integers.
IntMap<E>	Class IntMap represents a map with integer keys and generic type values.
IntSet	Class IntSet represents an indexed set of integers.
LongArray	Interface LongArray represents an immutable long[] array.
LowMafRefDiallelicGT	Class LowMafRefDiallelicGT represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.
LowMafRefGT	Class LowMafRefGT represent represents phased, non-missing genotypes for a list of reference samples at a single marker.
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.
Marker	Interface Marker represents a genetic marker.
MarkerContainer	Interface MarkerContainer represents an object that stores a unique vcf.Marker instance.
MarkerMap	Class MarkerMap represents genetic map positions for a list of markers.
Markers	Class Markers represent a list of markers in chromosome order.
PackedIntArray	Class PackedIntArray represents an immutable array of nonnegative integer values, which are stored in compressed form.
Pair<F,S>	Class Pair represents a pair of ordered objects.
Par	Class Parameters represents the parameters for a Beagle analysis.
Pedigree	Class Pedigree stores parent-offspring relationships in a list of samples.
Phase	Class Phase represents the equivalence of two phased genotypes for a marker or for a set of markers.
PhaseBaum1	Class PhaseBaum1 implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model.
PhaseData	Class PhaseData contains the input data for phasing genotypes.
PhaseIbs	Class PhaseIbs identifies haplotypes that share a long IBS segment with a specified haplotype.
PhaseLS	Class PhaseLS estimated genotypes phase using a haploid Li and Stephens hidden Markov model.
PhaseStates	Class PhaseStates identifies a rolling window of reference haplotypes for a target sample.
PlinkGenMap	Class PlinkGenMap 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.
R2Estimator	Class R2Estimator estimates the correlation between the estimated allele dose and true allele dose for a set of genotypes.
RefGT	Interface RefGT represents phased, compressed, nonmissing genotype data for a list of markers and a list of reference samples.
RefGTRec	Interface RefGTRec represents represents phased genotype data for one marker.
RefHapHash	Class RefHapHash stores a hash code for each haplotype in a sublist of reference haplotypes.
RefIt	Class RefIt represents an iterator whose next() method returns an object storing data from a VCF record with phased, non-missing genotypes.
Regress	Class Regress estimates a regression coefficient.
RestrictedVcfWindow	Class RestrictedVcfWindow represents a sliding window of VCF records.
RunStats	Class RunStats contains methods for storing and printing statistics describing a Beagle analysis.
SampleFileIt<E>	An iterator for records in a file.
SampleIds	Class SampleIds is a singleton class that represents a list of sample identifiers.
Samples	Class Samples stores a list of samples.
SeqCodedRefGT	Class SeqCodedRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker.
SeqCoder3	Class SeqCoder3 compresses a sequence of allele-coded RefGTRec objects.
SplicedGT	Class SplicedGT represents genotype emission probabilities for a set of samples.
StateProbs	Class StateProbs stores a subset of Li and Stephens HMM states and associated probabilities for a target haplotype.
StateProbsFactory	Class StateProbsFactory stores HMM state probabilities that that can be used to imputed impute missing HMM state probabilities using linear interpolation.
StringUtil	Class StringUtil is a utility class with static methods for counting and returning delimited fields in a string.
TargetData	Class TargetData represents a sliding window of target VCF records.
ThreadSafeIndexer<T>	Class ThreadSafeIndexer indexes objects.
UnBref3	Class UnBref3 converts files in bref version 3 format into VCF format.
UnsignedByteArray	Class ShiftedByteIndexArray represents an immutable array of integer values between 0 and 255 inclusive that is stored as a byte[] array whose values have been translated by -128.
Utilities	Class Utilities contains miscellaneous static utility methods.
Validate	Class Validate contains static methods for validating command line arguments.
VcfHeader	Class VcfHeader represents the Variant Call Format (VCF) meta-information lines and the Variant Call Format header line that precede the first Variant Call Format record.
VcfIt<E extends MarkerContainer>	Class VcfIt represents an iterator whose next() method returns an object storing data from a VCF record.
VcfMetaInfo	Class VcfMetaInfo represents a VCF meta-information line.
VcfRecBuilder	Class VcfRecBuilder contains methods for constructing and printing a VCF record in VCF 4.2 format.
VcfRecGTParser	Class VcfRecGTParser parses VCF records and extracts the GT format field.
VcfRecord	Class VcfRecord represents a VCF record.
VcfWriter	Class VcfWriter contains static methods for writing data in VCF 4.2 format.
Window<E extends GTRec>	Class Window represents a window of VCF recList.
WindowIt<E extends GTRec>	Class WindowIt represents a sliding window of VCF recList.
WindowWriter	Class WindowWriter writes VCF and IBD output data.
WrappedHapPair	Class WrappedHapPair is a HapPair instance that wraps a RefGTWindow object.
WrappedIntArray	Class WrappedIntArray represents an immutable int[] array.