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