All Classes

Class	Description
AsIsBref3Writer	Class AsIsBref3Writer writes VCF data with phased, non-missing genotypes to a binary reference format v3 (bref) file.
BasicGT	Class BasicGT represents genotypes for a list of markers and samples.
BasicGTRec	Class BasicGTRec stores genotypes for a list of samples at a single marker.
BasicMarker	Class BasicMarker represents a genetic marker.
BasicPhaseStates	Class BasicPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype or target sample.
BGZIPOutputStream	Class BGZIPOutputStream is an output stream filter that performs BGZIP compression.
BitArray	Interface BitArray represents a mutable sequence of bits with a fixed length.
BitArrayGTRec	Class BitArrayGT represents genotypes for a list of samples at a single marker.
BitArrayRefGTRec	Class BitArrayRefGTRec represents phased, nonmissing, genotypes for a list of samples at a single marker.
BlockLineReader	Class BlockLineReader is a blbutil.FileIt that reads blocks of lines from a file.
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.
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 input genotype data and the current estimated phased genotypes for each target sample.
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.
FwdPbwtPhaser	Class FwdPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT).
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.
HaplotypeCoder	Class HaplotypeCoder indexes the observed allele sequences in phased reference and target genotype data in a chromosome interval.
HmmParamData	Class HmmParamData generates data for estimating allele mismatch and recombination intensity parameters for a haploid Li and Stephens hidden Markov model.
HmmStateProbs	Class HmmStateProbs has a method that returns the reference haplotype and probability associated with each HMM state.
HmmUpdater	Class HmmUpdater has static methods for next marker updates of forward and backward HMM values.
Ibs2	Class Ibs2 stores IBS2 segments that any target sample shares with another target sample.
Ibs2Markers	Class Ibs2Markers stores the markers and intervals that are used to detect IBS2 segments.
Ibs2Sets	Class Ibs2Sets partitions markers into steps, and stores the sets of samples whose genotypes are consistent with IBS2 in each step.
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.
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.
LowFreqPbwtPhaseIbs	Class AltPbwtPhaseIBS uses the Positional Burrows-Wheeler Transform (PBWT) and rare variants to select IBS haplotypes for each sample for each specified genomic interval.
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.
LowFreqPhaseStates	Class LowFreqPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype.
LowMafDiallelicGTRec	Class LowMafDiallelicGTRc stores genotypes for a list of samples at a diallelic marker.
LowMafGTRec	Class LowMafGTRc stores genotypes for a list of samples at a marker.
LowMafRefDiallelicGTRec	Class LowMafRefDiallelicGTRec represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.
LowMafRefGTRec	Class LowMafRefGTRec 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.
Marker	Interface Marker represents a genetic marker.
MarkerCluster	Class MarkerCluster represents a partition of markers into contiguous marker clusters.
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 genetic distances for a sequence of genomic loci.
Markers	Class Markers represent a list of markers in chromosome order.
MultiThreadUtils	Class Utilities contains miscellaneous static utility methods for multi-threaded programming.
PackedIntArray	Class PackedIntArray represents an immutable array of nonnegative integer values, which are stored in compressed form.
Par	Class Parameters represents the parameters for a Beagle analysis.
ParamEstimates	Class ParamEstimates estimates the allele mismatch probability and the recombination intensity for a haploid Li and Stephens hidden Markov model.
PbwtDivUpdater	Class PbwtDivUpdater updates prefix and divergence arrays using the positional Burrows-Wheeler transform (PBWT).
PbwtIbsData	Class PbwtIbsData contains parameters and data for finding haplotypes that share an IBS segment with a target haplotype.
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.
PbwtPhaser	Class PbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT)
PbwtRecPhaser	Class PbwtRecPhaser partially phases and imputes genotypes using the Positional Burrows-Wheeler transform.
PbwtUpdater	Class PbwtDivUpdater updates prefix arrays using the positional Burrows-Wheeler transform (PBWT).
Pedigree	Class Pedigree stores parent-offspring relationships in a list of samples.
PhaseBaum1	Class PhaseBaum1 implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model.
PhaseData	Class PhaseData stores the current genotype phase estimates and parameter values.
PhaseLS	Class PhaseLS contains static methods for estimated genotypes phase using a haploid Li and Stephens hidden Markov model.
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.
RefGT	Class RefGT 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.
RefTargSlidingWindow	Class RefTargSlidingWindow represents a sliding window of reference and target VCF records.
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.
RevPbwtPhaser	Class RevPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT).
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.
SamplePhase	Each instance of class SamplePhase stores an estimated haplotype pair for a sample, the list of markers with missing genotypes for the sample, a list of markers whose genotype phase with respect to the preceding heterozygote genotype is considered to be uncertain for the sample, and a set of marker clusters for the sample.
Samples	Class Samples stores a list of samples.
SampleSeg	Class SampleSeg represents a segment of genotype data in 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.
SlidingWindow	Interface SlidingWindow represents a sliding window of VCF records.
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.
Stage2Baum	Class Stage2Baum 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.
Stage2Haps	Class Stage2Haps stores phased genotypes.
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.
Steps	Class Steps represents a partition of a list of markers into a sequence of sets of consecutive markers (the steps).
StringUtil	Class StringUtil is a utility class with static methods for counting and returning delimited fields in a string.
SynchedIntList	Class SynchedIntList represents a list of integers.
TargSlidingWindow	Class TargSlidingWindow 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 UnsignedByteIndexArray 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 GTRec>	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 VcfRec 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.
VcfRecGTParser.HapListRep
VcfWriter	Class VcfWriter contains static methods for writing data in VCF 4.2 format.
Window	Interface Window1 represents a sliding window of target VCF records or a sliding window of reference and target VCF records.
WindowWriter	Class WindowWriter writes VCF and IBD output data.
WrappedIntArray	Class WrappedIntArray represents an immutable int[] array.
XRefGT	Class XRefGT represents phased, non-missing genotypes for a list of samples that are stored in column-major (i.e.