Interface | Description |
---|---|
AL |
Interface
AL (Allele Likelihoods) represents allele
likelihoods for a set of haplotypes. |
Data |
Interface
Data represents a sliding window of target VCF records
or a sliding window of reference and target VCF records. |
GL |
Interface
GL (Genotype Likelihoods) represents genotype
likelihoods for a set of samples. |
HapsMarker |
Interface
HapsMarker represents marker alleles for a
list of haplotype pairs. |
Marker |
Interface
Marker represents a genetic marker. |
MarkerContainer |
Interface
MarkerContainer represents an object that stores
a unique vcf.Marker instance. |
VcfEmission |
Interface
VcfEmission represents genotype emission
probabilities for a set of samples at a single marker. |
Class | Description |
---|---|
AllData |
Class
AllData represents a sliding window of
reference and target VCF records. |
BasicGL |
Class
BasicGL represents genotype emission probabilities
for a set of samples. |
BasicMarker |
Class
BasicMarker represents a genetic marker. |
BitSetGT |
Class
BitSetGT represents genotype emission
probabilities for a list of samples at a single marker. |
BitSetRefGT |
Class
BitSetRefGT represents genotype emission
probabilities for a list reference samples with phased, non-missing
genotypes at a single marker. |
Bref |
Class
Bref has methods for reading and writing phased,
non-missing genotypes that are stored in a "bref" binary VCF file. |
BrefIt |
Class
BrefIt represents an iterator whose next()
method returns an object storing data from a VCF record with phased,
non-missing genotypes. |
ByteArrayRefGT |
Class
ByteArrayRefGT represents phased, non-missing
genotypes for a list of reference samples at a single marker. |
FilterUtil |
Class
FilterUtil contains static methods for constructing
marker filters. |
FuzzyGL |
Class
FuzzyGL is a wrapper for a GL
instance that incorporates a fixed error rate for the
observed (emitted) allele to differ from the true allele. |
GprobsStatistics |
Class
GprobsStatistics has methods for computing statistics
from posterior genotype probabilities. |
HbdAL |
Class
HbdAL represents allele emission probabilities
for a set of haplotype pairs under a homozygosity by descent (HBD) model. |
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. |
Markers |
Class
Markers represent a list of markers in chromosome order. |
MaskedEndsGL |
Class
MaskedEndsGL is a wrapper for a GL
instance that masks the genotype emission probabilities for a
user-specified number of starting and ending markers. |
NoPhaseGL |
Class
NoPhaseGL is a wrapper for a GL
instance that hides all genotype phase data in the wrapped object. |
R2Estimator |
Class
R2Estimator estimates the correlation between the
estimated allele dose and true allele dose for a set of genotypes. |
RefGL |
Class
RefGL represents genotype emission probabilities
for a reference panel of phased, non-missing 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. |
RevGL |
Class
RevGL is wrapper for a GL instance. |
SeqCodedRefGT |
Class
SeqCodedRefGT represents phased, non-missing
genotypes for a list of reference samples at a single marker. |
SplicedGL |
Class
SplicedGL represents genotype emission probabilities
for a set of samples. |
TargetData |
Class
TargetData represents a sliding window of
target VCF records. |
VcfEmissionCompressor |
Class
VcfEmissionCompressor compresses a sequence of
VcfEmission objects which contain reference genotype data. |
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. |
VcfWindow |
Class
VcfWindow represents a sliding window of VCF records. |
VcfWriter |
Class
VcfWriter contains static methods for writing data in
VCF 4.2 format. |