# Package htsjdk.variant.variantcontext

package htsjdk.variant.variantcontext

Related Packages
Package
Description
htsjdk.variant.variantcontext.filter
htsjdk.variant.variantcontext.writer
Class
Description
Allele
Immutable representation of an allele.
CommonInfo
Common utility routines for VariantContext and Genotype
FastGenotype
This class encompasses all the basic information about a 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.
GenotypeJEXLContext
GenotypeLikelihoods
GenotypeLikelihoods.GenotypeLikelihoodsAllelePair
GenotypesContext
Represents an ordered collection of Genotype objects
GenotypeType
Summary types for Genotype objects
JexlMissingValueTreatment
How to treat values that appear in a jexl expression but are missing in the context it's applied to
LazyGenotypesContext
Lazy-loading GenotypesContext.
LazyGenotypesContext.LazyData
Returns the data used in the full GenotypesContext constructor `GenotypesContext(java.util.ArrayList, java.util.Map, java.util.List)`
LazyGenotypesContext.LazyParser
Simple lazy parser interface.
SimpleAllele
An implementation of `Allele` which includes a byte[] of the bases in the allele or the symbolic name.
StructuralVariantType
Type of Structural Variant as defined in the VCF spec 4.2
VariantContext
High-level overview
VariantContext.Type
VariantContext.Validation
VariantContextBuilder
Builder class for `VariantContext`.
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.
VariantContextUtils
VariantContextUtils.JexlVCMatchExp
A simple but common wrapper for matching `VariantContext` objects using JEXL expressions