| 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.
|