Package vcf

Interface Summary

Interface	Description
Data	Interface Data represents a sliding window of target VCF records or a sliding window of reference and target VCF records.
DuplicatesGTRec	Interface DuplicatesGTRec represents marker alleles for a list of samples.
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.
Marker	Interface Marker represents a genetic marker.
MarkerContainer	Interface MarkerContainer represents an object that stores a unique vcf.Marker instance.
RefGT	Interface RefGT represents phased, compressed, nonmissing genotype data for a list of markers and a list of reference samples.
RefGTRec	Interface RefGTRec represents represents phased genotype data for one marker.
XGT1	Interface XGT1 (Genotype Likelihoods) represents genotype likelihoods for one sample.

Class Summary

Class	Description
AllData	Class AllData represents a sliding window of reference and target VCF recList.
BasicGT	Class BasicGT represents genotype emission probabilities for a set of samples.
BasicMarker	Class BasicMarker represents a genetic marker.
BasicRefGT	Class BasicRefGT stores a list of samples and a haplotype pair for each sample.
BitSetGT	Class BitSetGT represents genotype emission probabilities for a list of samples at a single marker.
FilterUtil	Class FilterUtil contains static methods for constructing marker filters.
IntervalVcfIt<E extends MarkerContainer>	Class IntervalVcfIterator is a sample file iterator whose next() method returns a marker container.
LowMafRefDiallelicGT	Class LowMafRefDiallelicGT represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.
LowMafRefGT	Class LowMafRefGT represent represents phased, non-missing genotypes for a list of reference samples at a single marker.
MarkerMap	Class MarkerMap represents genetic map positions for a list of markers.
Markers	Class Markers represent a list of markers in chromosome order.
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.
R2Estimator	Class R2Estimator estimates the correlation between the estimated allele dose and true allele dose for a set of genotypes.
RefIt	Class RefIt represents an iterator whose next() method returns an object storing data from a VCF record with phased, non-missing genotypes.
RestrictedVcfWindow	Class RestrictedVcfWindow represents a sliding window of VCF records.
SeqCodedRefGT	Class SeqCodedRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker.
SplicedGT	Class SplicedGT represents genotype emission probabilities for a set of samples.
TargetData	Class TargetData represents a sliding window of target VCF records.
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 MarkerContainer>	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.
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.
VcfRecord	Class VcfRecord represents a VCF record.
VcfWriter	Class VcfWriter contains static methods for writing data in VCF 4.2 format.
Window<E extends GTRec>	Class Window represents a window of VCF recList.
WindowIt<E extends GTRec>	Class WindowIt represents a sliding window of VCF recList.
XBasicGT	Class XBasicGT represents genotype and genotype emission probabilities for a set of samples optimized by sample.
XBasicGT1	Class XBasicGT1 represents genotype likelihoods for one sample.