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 | 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. |