All Classes
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All Classes Interface Summary Class Summary Class Description AllData ClassAllData
represents a sliding window of reference and target VCF records.AlleleImputer ClassAlleleImputer
imputes alleles from marker allele frequencies.AsIsBref3Writer ClassAsIsBref3Writer
writes VCF data with phased, non-missing genotypes to a binary reference format v3 (bref) file.BasicGT ClassBasicGT
represents genotype emission probabilities for a set of samples.BasicMarker ClassBasicMarker
represents a genetic marker.BestMatch ClassBestMatch
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 ClassBGZIPOutputStream
is an output stream filter that performs BGZIP compression.BitSetGTRec ClassBitSetGT
represents genotype emission probabilities for a list of samples at a single marker.Bref3 ClassBref3
converts files in VCF format into bref version 3 format.Bref3It ClassBref3It
represents an iterator whosenext()
which returns records from a bref version 3 file.Bref3Reader ClassBref3Reader
contains methods for reading a bref 3 (binary reference format) file.BrefBlock ClassBrefBlock
represents starting chromosome coordinates and file offset for the start of a binary reference format (bref) data block.BrefWriter InterfaceBrefWrites
writes phased, non-missing genotypes to a binary reference format (bref) file.CharArray /**ChromIds ClassChromIds
is a singleton class that represents a list of chromosome identifiers.ChromInterval ClassChromInterval
represents a chromosome interval whose end points are genome coordinates.CodedSteps ClassCodedSteps
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 ClassCodedSteps
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 ClassCompHapSegment
represents a copied haplotype segment in a composite reference haplotype.CompressBref3Writer ClassCompressBref3Writer
writes phased, non-missing genotypes to a binary reference format v3 (bref) file.Const ClassConst
provides public static final fields with string and character constants.Data InterfaceData
represents a sliding window of target VCF records or a sliding window of reference and target VCF records.DoubleArray ClassDoubleArray
represents an immutable list of double floating point values.DuplicatesGTRec InterfaceDuplicatesGTRec
represents marker alleles for a list of samples.EstPhase ClassEstPhase
stores original input genotype data.FileIt<E> An iterator for data elements in a file.FileUtil ClassFileUtil
contains static methods for working with files.Filter<E> A filter for accepting or rejecting objects.FilterUtil ClassFilterUtil
contains static methods for constructing marker filters.FixedPhaseData ClassFixedPhaseData
stores immutable data for a marker window.FloatArray ClassFloatArray
represents an immutable list of float floating point values.FloatList ClassFloatList
represents a list of floats.FwdBwd ClassFwdBwd
implements computes HMM reference haplotypes and state probabilities.GeneticMap InterfaceGeneticMap
represents a genetic map for one or more chromosomes.GT InterfaceGT
represents genotype data for a list of markers and a list of samples.GTRec InterfaceGTRec
represents represents genotype data for one marker.HapImputer ClassImputableHaps
performs imputation to estimate missing alleles and missing haplotype phase.HaplotypeCoder ClassHaplotypeCoder
indexes the observed allele sequences in phased reference and target genotype data in a chromosome interval.HapsGT ClassHapsGT
implements thevcf.GT
interface by storing the haplotypes as bit arrays.HmmUpdater Instances of classHmmUpdater
have methods for one-step updates of forward or backward HMM values.Ibs2 ClassIbs2
stores IBS2 segments that any target sample shares with another target or reference sample.ImpData ClassImpData
contains the input data for imputation of ungenotyped markers.ImpIbs ClassImpIbs
identifies haplotypes that share a long IBS segment with a specified haplotype.ImpLS ClassImpLS
computes HMM state probabilities at genotyped markers in the target haplotypes.ImpLSBaum ClassImpLSBaum
implements a Baum hidden Markov model forward and backward algorithms for computing HMM state probabilities at genotyped markers using IBS-matched reference haplotypes.ImpStates ClassImpStates
identifies a list of pseudo-reference haplotypes for a target haplotype.ImputeBaum ClassImputeBaum
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 ClassImputeRecBuilder
contains methods for constructing and printing a VCF record in VCF 4.3 format.ImputedVcfWriter ClassImputedVcfWriter
writes observed and imputed genotypes to a VCF output file.IndexArray ClassIndexArray
stores an array whose entries are elements of a bounded set of non-negative integers along with an upper bound.InputIt ClassInputIt
is a buffered iterator whosenext()
method returns lines of a text input stream.IntArray InterfaceIntArray
represents an immutableint[]
array.IntervalVcfIt<E extends MarkerContainer> ClassIntervalVcfIterator
is a sample file iterator whosenext()
method returns a marker container.IntInterval InterfaceIntInterval
represents an interval of consecutive integers.IntIntMap ClassIntIntMap
represents a map with integer keys and integer values.IntList ClassIntList
represents a list of integers.LongArray InterfaceLongArray
represents an immutablelong[]
array.LowFreqPhaseIbs ClassLowFreqPhaseIbs
identifies haplotypes that share a long IBS segment or a low frequency variant with a specified haplotype in a specified genomic interval.LowMafRefDiallelicGTRec ClassLowMafRefDiallelicGT
represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.LowMafRefGTRec ClassLowMafRefGT
represent represents phased, non-missing genotypes for a list of reference samples at a single marker.Main ClassMain
is the entry class for the Beagle program.MainHelper ClassMainHelper
is an auxiliary class with methods called by themain.Main
class.Marker InterfaceMarker
represents a genetic marker.MarkerContainer InterfaceMarkerContainer
represents an object that stores a uniquevcf.Marker
instance.MarkerIndices ClassMarkerIndices
stores the overlap with adjacent marker windows and the mappings between marker indices and the target marker indices.MarkerMap ClassMarkerRecombMap
represents genetic map positions and inter-marker haplotype switch probabilities for a sequence of genomic loci.Markers ClassMarkers
represent a list of markers in chromosome order.MultiThreadUtils ClassUtilities
contains miscellaneous static utility methods for multi-threaded programming.PackedIntArray ClassPackedIntArray
represents an immutable array of nonnegative integer values, which are stored in compressed form.Pair<F,S> ClassPair
represents a pair of ordered objects.Par ClassParameters
represents the parameters for a Beagle analysis.PbwtPhaseIbs ClassPbwtPhaseIBS
uses the Positional Burrows-Wheeler Transform (PBWT) to find long IBS haplotypes for each sample that contain a specified small genomic interval.PbwtUpdater ClassPbwtUpdater
updates prefix and divergence arrays using the positional Burrows-Wheeler transform (PBWT).Pedigree ClassPedigree
stores parent-offspring relationships in a list of samples.PhaseBaum1 ClassPhaseBaum1
implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model.PhaseData ClassPhaseData
contains the current input data for updating genotype phase.PhaseIbs Instances of interfacePhaseIbs
identify haplotypes that are identical by state with a specified haplotype in a specified genomic interval.PhaseLS ClassPhaseLS
estimated genotypes phase using a haploid Li and Stephens hidden Markov model.PhaseStates ClassPhaseStates
has methods for constructing a Li and Stephens HMM for a target haplotype or target sample.PlinkGenMap ClassPlinkGenMap
represents a genetic map derived from a PLINK map file with map positions in cM units for one or more chromosomes.PositionMap ClassPositionMap
represents a genetic map obtained by multiplying chromosome position by a scale factor.RecombRegress ClassRecombRegress
uses linear regression to estimate the recombination factor for a haploid Li and Stephens hidden Markov model.RefGT ClassBasicRefGT
stores a list of samples and a haplotype pair for each sample.RefGTRec InterfaceRefGTRec
represents represents phased genotype data for one marker.RefHapHash ClassRefHapHash
stores a hash code for each haplotype in a sublist of reference haplotypes.RefIt ClassRefIt
represents an iterator whosenext()
method returns an object storing data from a VCF record with phased, non-missing genotypes.Regress ClassRegress
estimates a regression coefficient.RestrictedGT ClassRestrictedGT
is a wrapper for aGT
instance that restricts the data to a subset of the VCF records.RestrictedVcfWindow ClassRestrictedVcfWindow
represents a sliding window of VCF records.RunStats ClassRunStats
contains methods for storing and printing statistics describing a Beagle analysis.SampleFileIt<E> An iterator for records in a file.SampleIds ClassSampleIds
is a singleton class that represents a list of sample identifiers.Samples ClassSamples
stores a list of samples.SampleSeg ClassSampleSeg
represents a haplotype shared with a sample.SeqCodedRefGTRec ClassSeqCodedRefGT
represents phased, non-missing genotypes for a list of reference samples at a single marker.SeqCoder3 ClassSeqCoder3
compresses a sequence of allele-codedRefGTRec
objects.SplicedGT ClassSplicedGT
represents genotypes for a set of samples that are obtained by replacing the initial markers of oneGT
instance with phased genotypes from anotherGT
instance.StateProbs ClassStateProbs
stores a subset of Li and Stephens HMM states and associated probabilities for a target haplotype.StateProbsFactory ClassStateProbsFactory
stores HMM state probabilities that that can be used to imputed impute missing HMM state probabilities using linear interpolation.StringUtil ClassStringUtil
is a utility class with static methods for counting and returning delimited fields in a string.TargetData ClassTargetData
represents a sliding window of target VCF records.ThreadSafeIndexer<T> ClassThreadSafeIndexer
indexes objects.UnBref3 ClassUnBref3
converts files in bref version 3 format into VCF format.UnsignedByteArray ClassShiftedByteIndexArray
represents an immutable array of integer values between 0 and 255 inclusive that is stored as abyte[]
array whose values have been translated by -128.Utilities ClassUtilities
contains miscellaneous static utility methods.Validate Class Validate contains static methods for validating command line arguments.VcfHeader ClassVcfHeader
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> ClassVcfIt
represents an iterator whosenext()
method returns an object storing data from a VCF record.VcfMetaInfo ClassVcfMetaInfo
represents a VCF meta-information line.VcfRec ClassVcfRecord
represents a VCF record.VcfRecBuilder ClassVcfRecBuilder
contains methods for constructing and printing a VCF record in VCF 4.2 format.VcfRecGTParser ClassVcfRecGTParser
parses VCF records and extracts the GT format field.VcfWriter ClassVcfWriter
contains static methods for writing data in VCF 4.2 format.Window<E extends GTRec> ClassWindow
represents a window of VCF records.WindowIt<E extends GTRec> ClassWindowIt
represents a sliding window of VCF recList.WindowWriter ClassWindowWriter
writes VCF and IBD output data.WrappedIntArray ClassWrappedIntArray
represents an immutableint[]
array.