All Classes and Interfaces

Class
Description
AlleleRefGTRec
Class AlleleRefGTRec represent represents phased, non-missing genotypes for a list of reference samples at a single marker.
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.
BasicPhaseStates
Class BasicPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype or target sample.
BGZipIt
Class BGZipIt is a blbutil.FileIt<String> whose next() method returns lines of a bgzip-compressed file.
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.
Bref3Header
Class Bref3Header represents the header of a bref3 file (binary reference format version 3).
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 bref3 (binary reference format version 3) 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.
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.
HapRefGTRec
Class HapRefGTRec represents phased, non-missing genotypes for a list of reference samples at a single marker.
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.
IntArrayRefGTRec
Class IntArrayRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker.
IntervalVcfIt<E>
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 LowFreqPbwtPhaseIbs 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.
Main
Class Main is the entry class for the Beagle program.
Marker
Class Marker represents a VCF record's CHROM, POS, ID, REF, ALT, QUAL, FILTER, and INFO fields.
MarkerCluster
Class MarkerCluster represents a partition of markers into contiguous marker clusters.
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.
MarkerParser
Class MarkerParser is a parser and filter for a VCF record's ID, REF, ALT, QUAL, FILTER, and INFO subfields.
Markers
Class Markers represent a list of markers in chromosome order.
MarkerUtils
Class MarkerUtils contains static helper methods for the Marker class.
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.
PhaseBaum
Interface PhaseBaum updates the estimated genotype phase of specified samples.
PhaseBaum2
Interface PhaseBaum2 updates the estimated genotype phase of specified samples.
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.
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.
SamplePhase.ClustType
 
Samples
Class Samples stores a list of samples.
SampleSeg
Class SampleSeg represents a segment of genotype data in a sample.
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.
SwapRate
Class SwapRate stores the proportion of unphased heterozygotes whose phase with respect to the previous heteroygote has been reversed.
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.
TriFunction<T,U,V,R>
Class TriFunction represents a function that accepts three arguments and produces a result.
TwoAlleleRefGTRec
Class TwoAlleleRefGTRec represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.
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.
Utilities
Class Utilities contains miscellaneous static utility methods.
Validate
Class Validate contains static methods for validating command line arguments.
VcfFileIt<E>
An iterator for records in a VCF file.
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>
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
Class Window 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.