Package vcf
package vcf
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ClassDescriptionClass
BasicGT
represents genotypes for a list of markers and samples.ClassBasicGTRec
stores genotypes for a list of samples at a single marker.ClassBasicMarker
represents a genetic marker.ClassBitArrayGT
represents genotypes for a list of samples at a single marker.ClassBitArrayRefGTRec
represents phased, nonmissing, genotypes for a list of samples at a single marker.InterfaceDuplicatesGTRec
represents marker alleles for a list of samples.ClassFilterUtil
contains static methods for constructing marker filters.InterfaceGeneticMap
represents a genetic map for one or more chromosomes.InterfaceGT
represents genotype data for a list of markers and a list of samples.InterfaceGTRec
represents represents genotype data for one marker.IntervalVcfIt<E extends MarkerContainer>ClassIntervalVcfIterator
is a sample file iterator whosenext()
method returns a marker container.ClassLowMafDiallelicGTRc
stores genotypes for a list of samples at a diallelic marker.ClassLowMafGTRc
stores genotypes for a list of samples at a marker.ClassLowMafRefDiallelicGTRec
represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.ClassLowMafRefGTRec
represent represents phased, non-missing genotypes for a list of reference samples at a single marker.InterfaceMarker
represents a genetic marker.InterfaceMarkerContainer
represents an object that stores a uniquevcf.Marker
instance.ClassMarkerIndices
stores the overlap with adjacent marker windows and the mappings between marker indices and the target marker indices.ClassMarkerRecombMap
represents genetic map positions and inter-marker genetic distances for a sequence of genomic loci.ClassMarkers
represent a list of markers in chromosome order.ClassPlinkGenMap
represents a genetic map derived from a PLINK map file with map positions in cM units for one or more chromosomes.ClassPositionMap
represents a genetic map obtained by multiplying chromosome position by a scale factor.ClassRefGT
stores a list of samples and a haplotype pair for each sample.InterfaceRefGTRec
represents represents phased genotype data for one marker.ClassRefIt
represents an iterator whosenext()
method returns an object storing data from a VCF record with phased, non-missing genotypes.ClassRefTargSlidingWindow
represents a sliding window of reference and target VCF records.ClassRestrictedGT
is a wrapper for aGT
instance that restricts the data to a subset of the VCF records.ClassRestrictedVcfWindow
represents a sliding window of VCF records.ClassSamples
stores a list of samples.ClassSeqCodedRefGT
represents phased, non-missing genotypes for a list of reference samples at a single marker.InterfaceSlidingWindow
represents a sliding window of VCF records.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.ClassSteps
represents a partition of a list of markers into a sequence of sets of consecutive markers (the steps).ClassTargSlidingWindow
represents a sliding window of target VCF records.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.ClassVcfIt
represents an iterator whosenext()
method returns an object storing data from a VCF record.ClassVcfMetaInfo
represents a VCF meta-information line.ClassVcfRec
represents a VCF record.ClassVcfRecBuilder
contains methods for constructing and printing a VCF record in VCF 4.2 format.ClassVcfRecGTParser
parses VCF records and extracts the GT format field.ClassVcfWriter
contains static methods for writing data in VCF 4.2 format.InterfaceWindow1
represents a sliding window of target VCF records or a sliding window of reference and target VCF records.ClassXRefGT
represents phased, non-missing genotypes for a list of samples that are stored in column-major (i.e.