Package vcf

package vcf
  • Class
    Description
    AlleleRefGTRec
    Class AlleleRefGTRec represent represents phased, non-missing genotypes for a list of reference samples at a single marker.
    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.
    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.
    FilterUtil
    Class FilterUtil contains static methods for constructing marker filters.
    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.
    HapRefGTRec
    Class HapRefGTRec represents phased, non-missing genotypes for a list of reference samples at a single marker.
    IntArrayRefGTRec
    Class IntArrayRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker.
    IntervalVcfIt<E extends GTRec>
    Class IntervalVcfIterator is a sample file iterator whose next() method returns a marker container.
    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.
    Marker
    Class Marker represents a VCF record's CHROM, POS, ID, REF, ALT, QUAL, FILTER, and INFO fields.
    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.
    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.
    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.
    Samples
    Class Samples stores a list of samples.
    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.
    Steps
    Class Steps represents a partition of a list of markers into a sequence of sets of consecutive markers (the steps).
    TargSlidingWindow
    Class TargSlidingWindow represents a sliding window of target VCF records.
    TwoAlleleRefGTRec
    Class TwoAlleleRefGTRec represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.
    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 extends GTRec>
    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.
    XRefGT
    Class XRefGT represents phased, non-missing genotypes for a list of samples that are stored in column-major (i.e.