Package vcf


package vcf
  • Class
    Description
    Class BasicGT represents genotypes for a list of markers and samples.
    Class BasicGTRec stores genotypes for a list of samples at a single marker.
    Class BasicMarker represents a genetic marker.
    Class BitArrayGT represents genotypes for a list of samples at a single marker.
    Class BitArrayRefGTRec represents phased, nonmissing, genotypes for a list of samples at a single marker.
    Interface DuplicatesGTRec represents marker alleles for a list of samples.
    Class FilterUtil contains static methods for constructing marker filters.
    Interface GeneticMap represents a genetic map for one or more chromosomes.
    Interface GT represents genotype data for a list of markers and a list of samples.
    Interface GTRec represents represents genotype data for one marker.
    Class IntervalVcfIterator is a sample file iterator whose next() method returns a marker container.
    Class LowMafDiallelicGTRc stores genotypes for a list of samples at a diallelic marker.
    Class LowMafGTRc stores genotypes for a list of samples at a marker.
    Class LowMafRefDiallelicGTRec represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.
    Class LowMafRefGTRec represent represents phased, non-missing genotypes for a list of reference samples at a single marker.
    Interface Marker represents a genetic marker.
    Interface MarkerContainer represents an object that stores a unique vcf.Marker instance.
    Class MarkerIndices stores the overlap with adjacent marker windows and the mappings between marker indices and the target marker indices.
    Class MarkerRecombMap represents genetic map positions and inter-marker genetic distances for a sequence of genomic loci.
    Class Markers represent a list of markers in chromosome order.
    Class PlinkGenMap represents a genetic map derived from a PLINK map file with map positions in cM units for one or more chromosomes.
    Class PositionMap represents a genetic map obtained by multiplying chromosome position by a scale factor.
    Class RefGT stores a list of samples and a haplotype pair for each sample.
    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 RefTargSlidingWindow represents a sliding window of reference and target VCF records.
    Class RestrictedGT is a wrapper for a GT instance that restricts the data to a subset of the VCF records.
    Class RestrictedVcfWindow represents a sliding window of VCF records.
    Class Samples stores a list of samples.
    Class SeqCodedRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker.
    Interface SlidingWindow represents a sliding window of VCF records.
    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 Steps represents a partition of a list of markers into a sequence of sets of consecutive markers (the steps).
    Class TargSlidingWindow represents a sliding window of target VCF records.
    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.
    Class VcfMetaInfo represents a VCF meta-information line.
    Class VcfRec represents a VCF record.
    Class VcfRecBuilder contains methods for constructing and printing a VCF record in VCF 4.2 format.
    Class VcfRecGTParser parses VCF records and extracts the GT format field.
     
    Class VcfWriter contains static methods for writing data in VCF 4.2 format.
    Interface Window1 represents a sliding window of target VCF records or a sliding window of reference and target VCF records.
    Class XRefGT represents phased, non-missing genotypes for a list of samples that are stored in column-major (i.e.