Package | Description |
---|---|
htsjdk.variant.bcf2 | |
htsjdk.variant.variantcontext | |
htsjdk.variant.variantcontext.filter | |
htsjdk.variant.variantcontext.writer | |
htsjdk.variant.vcf |
Class and Description |
---|
Allele
Immutable representation of an allele.
|
GenotypeBuilder
A builder class for genotypes
Provides convenience setter methods for all of the Genotype field
values.
|
LazyGenotypesContext.LazyData
Returns the data used in the full GenotypesContext constructor
GenotypesContext.GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List) |
LazyGenotypesContext.LazyParser
Simple lazy parser interface.
|
VariantContext
High-level overview
|
Class and Description |
---|
Allele
Immutable representation of an allele.
|
CommonInfo
Common utility routines for VariantContext and Genotype
|
Genotype
This class encompasses all the basic information about a genotype.
|
GenotypeBuilder
A builder class for genotypes
Provides convenience setter methods for all of the Genotype field
values.
|
GenotypeLikelihoods |
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair |
GenotypesContext
Represents an ordered collection of Genotype objects
|
GenotypeType
Summary types for Genotype objects
|
LazyGenotypesContext.LazyData
Returns the data used in the full GenotypesContext constructor
GenotypesContext.GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List) |
LazyGenotypesContext.LazyParser
Simple lazy parser interface.
|
VariantContext
High-level overview
|
VariantContext.Type |
VariantContext.Validation |
VariantContextBuilder
Builder class for
VariantContext . |
VariantContextUtils.JexlVCMatchExp
A simple but common wrapper for matching VariantContext objects using JEXL expressions
|
Class and Description |
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VariantContext
High-level overview
|
Class and Description |
---|
Genotype
This class encompasses all the basic information about a genotype.
|
VariantContext
High-level overview
|
Class and Description |
---|
Allele
Immutable representation of an allele.
|
LazyGenotypesContext.LazyData
Returns the data used in the full GenotypesContext constructor
GenotypesContext.GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List) |
VariantContext
High-level overview
|
VariantContextComparator
A Comparator that orders VariantContexts by the ordering of the contigs/chromosomes in the List
provided at construction time, then by start position with each contig/chromosome.
|