All Classes and Interfaces

Class AsIsBref3Writer writes VCF data with phased, non-missing genotypes to a binary reference format v3 (bref) file.

Class BasicGTRec stores genotypes for a list of samples at a single marker.

Class BasicPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype or target sample.

Class BGZIPOutputStream is an output stream filter that performs BGZIP compression.

Class BitArrayGT represents genotypes for a list of samples at a single marker.

Class BlockLineReader is a blbutil.FileIt that reads blocks of lines from a file.

Class Bref3It represents an iterator whose next() which returns records from a bref version 3 file.

Class BrefBlock represents starting chromosome coordinates and file offset for the start of a binary reference format (bref) data block.

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Class ChromInterval represents a chromosome interval whose end points are genome coordinates.

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.

Class CompressBref3Writer writes phased, non-missing genotypes to a binary reference format v3 (bref) file.

Class DoubleArray represents an immutable list of double floating point values.

Class EstPhase stores input genotype data and the current estimated phased genotypes for each target sample.

Class FileUtil contains static methods for working with files.

Class FilterUtil contains static methods for constructing marker filters.

Class FloatArray represents an immutable list of float floating point values.

Class FwdPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT).

Interface GT represents genotype data for a list of markers and a list of samples.

Class HaplotypeCoder indexes the observed allele sequences in phased reference and target genotype data in a chromosome interval.

Class HmmStateProbs has a method that returns the reference haplotype and probability associated with each HMM state.

Class Ibs2 stores IBS2 segments that any target sample shares with another target sample.

Class Ibs2Sets partitions markers into steps, and stores the sets of samples whose genotypes are consistent with IBS2 in each step.

Class ImpIbs identifies haplotypes that share a long IBS segment with a specified haplotype.

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.

Class ImputeRecBuilder contains methods for constructing and printing a VCF record in VCF 4.3 format.

Class IndexArray stores an array whose entries are elements of a bounded set of non-negative integers along with an upper bound.

Interface IntArray represents an immutable int[] array.

Interface IntInterval represents an interval of consecutive integers.

Class IntList represents a list of integers.

Class LowFreqPhaseIbs identifies haplotypes that share a long IBS segment or a low frequency variant with a specified haplotype in a specified genomic interval.

Class LowMafDiallelicGTRc stores genotypes for a list of samples at a diallelic marker.

Class LowMafRefDiallelicGTRec represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.

Class Main is the entry class for the Beagle program.

Class MarkerCluster represents a partition of markers into contiguous marker clusters.

Class MarkerIndices stores the overlap with adjacent marker windows and the mappings between marker indices and the target marker indices.

Class Markers represent a list of markers in chromosome order.

Class PackedIntArray represents an immutable array of nonnegative integer values, which are stored in compressed form.

Class ParamEstimates estimates the allele mismatch probability and the recombination intensity for a haploid Li and Stephens hidden Markov model.

Class PbwtIbsData contains parameters and data for finding haplotypes that share an IBS segment with a target haplotype.

Class PbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT)

Class PbwtDivUpdater updates prefix arrays using the positional Burrows-Wheeler transform (PBWT).

Class PhaseBaum1 implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model.

Class PhaseLS contains static methods for estimated genotypes phase using a haploid Li and Stephens hidden Markov model.

Class PositionMap represents a genetic map obtained by multiplying chromosome position by a scale factor.

Interface RefGTRec represents represents phased genotype data for one marker.

Class RefIt represents an iterator whose next() method returns an object storing data from a VCF record with phased, non-missing genotypes.

Class RestrictedGT is a wrapper for a GT instance that restricts the data to a subset of the VCF records.

Class RevPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT).

An iterator for records in a file.

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.

Class SampleSeg represents a segment of genotype data in a sample.

Class SeqCoder3 compresses a sequence of allele-coded RefGTRec objects.

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.

Class Stage2Haps stores phased genotypes.

Class StateProbsFactory stores HMM state probabilities that that can be used to imputed impute missing HMM state probabilities using linear interpolation.

Class StringUtil is a utility class with static methods for counting and returning delimited fields in a string.

Class TargSlidingWindow represents a sliding window of target VCF records.

Class UnBref3 converts files in bref version 3 format into VCF format.

Class Utilities contains miscellaneous static utility methods.

An iterator for records in a VCF file.

Class VcfIt represents an iterator whose next() method returns an object storing data from a VCF record.

Class VcfRec represents a VCF record.

Class VcfRecGTParser parses VCF records and extracts the GT format field.

Class VcfWriter contains static methods for writing data in VCF 4.2 format.

Class WindowWriter writes VCF and IBD output data.

Class XRefGT represents phased, non-missing genotypes for a list of samples that are stored in column-major (i.e.