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