AllData |
Class AllData represents a sliding window of reference and
target VCF records.
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BasicGT |
Class BasicGT represents genotype emission probabilities
for a set of samples.
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BasicMarker |
Class BasicMarker represents a genetic marker.
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BitSetGTRec |
Class BitSetGT represents genotype emission
probabilities 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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HapsGT |
Class HapsGT implements the vcf.GT interface by
storing the haplotypes as bit arrays.
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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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LowMafRefDiallelicGTRec |
Class LowMafRefDiallelicGT represent represents phased,
non-missing genotypes for a list of reference samples at a single diallelic
marker.
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LowMafRefGTRec |
Class LowMafRefGT 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 haplotype switch probabilities 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 BasicRefGT 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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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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TargetData |
Class TargetData 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 VcfRecord 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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VcfWriter |
Class VcfWriter contains static methods for writing data in
VCF 4.2 format.
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Window<E extends GTRec> |
Class Window represents a window of VCF records.
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WindowIt<E extends GTRec> |
Class WindowIt represents a sliding window of VCF recList.
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