All Classes

Class	Description
AllData	Class AllData represents a sliding window of reference and target VCF records.
AlleleImputer	Class AlleleImputer imputes alleles from marker allele frequencies.
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.
BestMatch	Class BestMatch has methods for finding a haplotype that shares a long IBS sequence containing a specified genomic interval with a target haplotype and that originates from a sample which carries a rare variant in the specified genomic interval that is also carried by the target sample.
BGZIPOutputStream	Class BGZIPOutputStream is an output stream filter that performs BGZIP compression.
BitSetGTRec	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.
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.
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.
CompHapSegment	Class CompHapSegment represents a copied haplotype segment in a composite reference haplotype.
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.
Data	Interface Data represents a sliding window of target VCF records or a sliding window of reference and target VCF records.
DoubleArray	Class DoubleArray represents an immutable list of double floating point values.
DuplicatesGTRec	Interface DuplicatesGTRec represents marker alleles for a list of samples.
EstPhase	Class EstPhase stores original input genotype data.
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.
FixedPhaseData	Class FixedPhaseData stores immutable data for a marker window.
FloatArray	Class FloatArray represents an immutable list of float floating point values.
FloatList	Class FloatList represents a list of floats.
FwdBwd	Class FwdBwd implements computes HMM reference haplotypes and state probabilities.
GeneticMap	Interface GeneticMap represents a genetic map for one or more chromosomes.
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.
HapImputer	Class ImputableHaps performs imputation to estimate missing alleles and missing haplotype phase.
HaplotypeCoder	Class HaplotypeCoder indexes the observed allele sequences in phased reference and target genotype data in a chromosome interval.
HapsGT	Class HapsGT implements the vcf.GT interface by storing the haplotypes as bit arrays.
HmmUpdater	Instances of class HmmUpdater have methods for one-step updates of forward or backward HMM values.
Ibs2	Class Ibs2 stores IBS2 segments that any target sample shares with another target or reference 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.
ImputeBaum	Class ImputeBaum applies the forward and backward algorithms for a haploid Li and Stephens hidden Markov model at high-frequency markers, and imputes missing genotypes and heterozygote phase at low-frequency markers.
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.
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.
IntIntMap	Class IntIntMap represents a map with integer keys and integer values.
IntList	Class IntList represents a list of integers.
LongArray	Interface LongArray represents an immutable long[] array.
LowFreqPhaseIbs	Class LowFreqPhaseIbs identifies haplotypes that share a long IBS segment or a low frequency variant with a specified haplotype in a specified genomic interval.
LowMafRefDiallelicGTRec	Class LowMafRefDiallelicGT represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.
LowMafRefGTRec	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.
MarkerIndices	Class MarkerIndices stores the overlap with adjacent marker windows and the mappings between marker indices and the target marker indices.
MarkerMap	Class MarkerRecombMap represents genetic map positions and inter-marker haplotype switch probabilities for a sequence of genomic loci.
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.
PbwtPhaseIbs	Class PbwtPhaseIBS uses the Positional Burrows-Wheeler Transform (PBWT) to find long IBS haplotypes for each sample that contain a specified small genomic interval.
PbwtUpdater	Class PbwtUpdater updates prefix and divergence arrays using the positional Burrows-Wheeler transform (PBWT).
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 current input data for updating genotype phase.
PhaseIbs	Instances of interface PhaseIbs identify haplotypes that are identical by state with a specified haplotype in a specified genomic interval.
PhaseLS	Class PhaseLS estimated genotypes phase using a haploid Li and Stephens hidden Markov model.
PhaseStates	Class PhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype or 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.
RecombRegress	Class RecombRegress uses linear regression to estimate the recombination factor for a haploid Li and Stephens hidden Markov model.
RefGT	Class BasicRefGT stores a list of samples and a haplotype pair for each sample.
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.
RestrictedGT	Class RestrictedGT is a wrapper for a GT instance that restricts the data to a subset of the VCF records.
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.
SampleSeg	Class SampleSeg represents a haplotype shared with a sample.
SeqCodedRefGTRec	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 genotypes for a set of samples that are obtained by replacing the initial markers of one GT instance with phased genotypes from another GT instance.
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.
VcfRec	Class VcfRecord represents a VCF record.
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.
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 records.
WindowIt<E extends GTRec>	Class WindowIt represents a sliding window of VCF recList.
WindowWriter	Class WindowWriter writes VCF and IBD output data.
WrappedIntArray	Class WrappedIntArray represents an immutable int[] array.
XBasicGT	Class XBasicGT represents genotype and genotype emission probabilities for a set of samples optimized by sample.
XBasicGT1	Class XBasicGT1 represents genotype likelihoods for one sample.
XGT1	Interface XGT1 (Genotype Likelihoods) represents genotype likelihoods for one sample.