Uses of Package
htsjdk.variant.variantcontext

Packages that use htsjdk.variant.variantcontext

Package	Description
htsjdk.variant.bcf2
htsjdk.variant.variantcontext
htsjdk.variant.variantcontext.filter
htsjdk.variant.variantcontext.writer
htsjdk.variant.vcf

Classes in htsjdk.variant.variantcontext used by htsjdk.variant.bcf2

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

Classes in htsjdk.variant.variantcontext used by htsjdk.variant.variantcontext

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

Classes in htsjdk.variant.variantcontext used by htsjdk.variant.variantcontext.filter

Class and Description
VariantContext High-level overview

Classes in htsjdk.variant.variantcontext used by htsjdk.variant.variantcontext.writer

Class and Description
Genotype This class encompasses all the basic information about a genotype.
VariantContext High-level overview

Classes in htsjdk.variant.variantcontext used by htsjdk.variant.vcf

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.