All Classes
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All Classes Interface Summary Class Summary Enum Summary Class Description AllData ClassAllData
represents a sliding window of reference and target VCF recList.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.BasicRefGT ClassBasicRefGT
stores a list of samples and a haplotype pair for each sample.BGZIPOutputStream ClassBGZIPOutputStream
is an output stream filter that performs BGZIP compression.BitHapPair ClassBitHapPair
represents a pair of haplotypes for a sample.BitSetGT 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.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.CurrentData ClassCurrentData
represents input data for the current marker window.Data InterfaceData
represents a sliding window of target VCF records or a sliding window of reference and target VCF records.DuplicatesGTRec InterfaceDuplicatesGTRec
represents marker alleles for a list of samples.EstPhase ClassEstPhase
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 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.FloatArray ClassFloatArray
represents an immutable list of float floating point values.FloatList ClassFloatList
represents a list of floats.GeneticMap InterfaceGeneticMap
represents a genetic map for one or more chromosomes.GenotypeValues InterfaceGenotypeValues
represents a value for each possible genotype for each sample at each marker.GT InterfaceGT
represents genotype data for a list of markers and a list of samples.GTRec InterfaceGTRec
represents represents genotype data for one marker.HaplotypeCoder ClassHaplotypeCoder
indexes the observed allele sequences in phased reference and target genotype data in a chromosome interval.HapPair InterfaceHapPair
represents a pair of haplotypes for a sample.HapPairPhasedGT ClassHapPairPhasedGT
stores a list of samples and a haplotype pair for each 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.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.InitTargHapPairs ClassInitTargHapPairs
has a static method for returning initial target haplotype pairs.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.IntList ClassIntList
represents a list of integers.IntMap<E> ClassIntMap
represents a map with integer keys and generic type values.IntSet ClassIntSet
represents an indexed set of integers.LongArray InterfaceLongArray
represents an immutablelong[]
array.LowMafRefDiallelicGT ClassLowMafRefDiallelicGT
represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.LowMafRefGT 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.MarkerMap ClassMarkerMap
represents genetic map positions for a list of markers.Markers ClassMarkers
represent a list of markers in chromosome order.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.Pedigree ClassPedigree
stores parent-offspring relationships in a list of samples.Phase ClassPhase
represents the equivalence of two phased genotypes for a marker or for a set of markers.PhaseBaum1 ClassPhaseBaum1
implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model.PhaseData ClassPhaseData
contains the input data for phasing genotypes.PhaseIbs ClassPhaseIbs
identifies haplotypes that share a long IBS segment with a specified haplotype.PhaseLS ClassPhaseLS
estimated genotypes phase using a haploid Li and Stephens hidden Markov model.PhaseStates ClassPhaseStates
identifies a rolling window of reference haplotypes for a 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.R2Estimator ClassR2Estimator
estimates the correlation between the estimated allele dose and true allele dose for a set of genotypes.RefGT InterfaceRefGT
represents phased, compressed, nonmissing genotype data for a list of markers and a list of reference samples.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.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.SeqCodedRefGT 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 genotype emission probabilities for a set of samples.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 MarkerContainer> ClassVcfIt
represents an iterator whosenext()
method returns an object storing data from a VCF record.VcfMetaInfo ClassVcfMetaInfo
represents a VCF meta-information line.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.VcfRecord ClassVcfRecord
represents a VCF record.VcfWriter ClassVcfWriter
contains static methods for writing data in VCF 4.2 format.Window<E extends GTRec> ClassWindow
represents a window of VCF recList.WindowIt<E extends GTRec> ClassWindowIt
represents a sliding window of VCF recList.WindowWriter ClassWindowWriter
writes VCF and IBD output data.WrappedHapPair ClassWrappedHapPair
is aHapPair
instance that wraps aRefGTWindow
object.WrappedIntArray ClassWrappedIntArray
represents an immutableint[]
array.XBasicGT ClassXBasicGT
represents genotype and genotype emission probabilities for a set of samples optimized by sample.XBasicGT1 ClassXBasicGT1
represents genotype likelihoods for one sample.XGT1 InterfaceXGT1
(Genotype Likelihoods) represents genotype likelihoods for one sample.