#Htsjdk.variant.variantcontext Classes and Interfaces

_{#Htsjdk.variant.variantcontext Classes and Interfaces - 58 results found.}

Name	Description	Type	Package	Framework
Allele	Immutable representation of an allele.	Class	htsjdk.variant.variantcontext	HtsJDK
AsyncVariantContextWriter	AsyncVariantContextWriter that can be wrapped around an underlying AsyncVariantContextWriter to provide asynchronous output.	Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2Encoder	See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldEncoder	See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldEncoder .AtomicInt		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldEncoder .Flag		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldEncoder .Float		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldEncoder .GenericInts		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldEncoder .IntArray		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldEncoder .StringOrCharacter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter	See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter .FTGenotypesWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter .GenericSiteWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter .GenotypesWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter .GTWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter .IGFGenotypesWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter .IntegerTypeGenotypesWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter .SiteWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriter .StaticallyTypeGenotypesWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
BCF2FieldWriterManager	See #BCFWriter for documentation on this classes role in encoding BCF2 filesSince:06/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
CommonInfo	Common utility routines for VariantContext and GenotypeAuthor:depristoSee Also:Serialized Form	Class	htsjdk.variant.variantcontext	HtsJDK
CompoundFilter	A Predicate on VariantContexts that returns true when either all its sub-predicates are true, or none are false.	Class	htsjdk.variant.variantcontext.filter	HtsJDK
FastGenotype	This class encompasses all the basic information about a genotype.	Class	htsjdk.variant.variantcontext	HtsJDK
FilteringIterator	A filtering iterator for VariantContexts that takes a base iterator and a VariantContextFilter.	Class	htsjdk.variant.variantcontext.filter	HtsJDK
Genotype	This class encompasses all the basic information about a genotype.	Class	htsjdk.variant.variantcontext	HtsJDK
GenotypeBuilder	A builder class for genotypes Provides convenience setter methods for all of the Genotype field	Class	htsjdk.variant.variantcontext	HtsJDK
GenotypeLikelihoods		Class	htsjdk.variant.variantcontext	HtsJDK
GenotypeLikelihoods .GenotypeLikelihoodsAllelePair		Class	htsjdk.variant.variantcontext	HtsJDK
GenotypeQualityFilter	A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).	Class	htsjdk.variant.variantcontext.filter	HtsJDK
GenotypesContext	Represents an ordered collection of Genotype objectsSee Also:Serialized Form	Class	htsjdk.variant.variantcontext	HtsJDK
GenotypeType	Summary types for Genotype objectsSince:Date createdAuthor:Your Name	Class	htsjdk.variant.variantcontext	HtsJDK
HeterozygosityFilter	A Predicate on VariantContexts that either returns true at heterozygous sites (invertible to false).	Class	htsjdk.variant.variantcontext.filter	HtsJDK
IntGenotypeFieldAccessors	A convenient way to provide a single view on the many int and int[] field values we work with, for writing out the values.	Class	htsjdk.variant.variantcontext.writer	HtsJDK
IntGenotypeFieldAccessors .Accessor		Class	htsjdk.variant.variantcontext.writer	HtsJDK
IntGenotypeFieldAccessors .ADAccessor		Class	htsjdk.variant.variantcontext.writer	HtsJDK
IntGenotypeFieldAccessors .DPAccessor		Class	htsjdk.variant.variantcontext.writer	HtsJDK
IntGenotypeFieldAccessors .GQAccessor		Class	htsjdk.variant.variantcontext.writer	HtsJDK
IntGenotypeFieldAccessors .PLAccessor		Class	htsjdk.variant.variantcontext.writer	HtsJDK
JavascriptVariantFilter	javascript based variant filter The script puts the following variables in the script context:	Class	htsjdk.variant.variantcontext.filter	HtsJDK
LazyGenotypesContext	Lazy-loading GenotypesContext.	Class	htsjdk.variant.variantcontext	HtsJDK
LazyGenotypesContext .LazyData	Returns the data used in the full GenotypesContext constructor GenotypesContext.	Class	htsjdk.variant.variantcontext	HtsJDK
LazyGenotypesContext .LazyParser	Simple lazy parser interface.	Interface	htsjdk.variant.variantcontext	HtsJDK
Options	Available writer options for VariantContextWritersSince:5/12Author:Mark DePristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK
PassingVariantFilter	A Predicate on VariantContexts that returns true at sites that are either unfiltered, or passing (as variants).	Class	htsjdk.variant.variantcontext.filter	HtsJDK
SnpFilter	A Predicate on VariantContexts that returns true at sites that are SNPsAuthor:Yossi Farjoun	Class	htsjdk.variant.variantcontext.filter	HtsJDK
SortingVariantContextWriter		Class	htsjdk.variant.variantcontext.writer	HtsJDK
VariantContext	High-level overview The VariantContext object is a single general class system for representing genetic variation data composed of:	Class	htsjdk.variant.variantcontext	HtsJDK
VariantContext .Type	See Also:NCBI Handbook dbSNP variation classRules for assigning allele classesSample allele definition	Class	htsjdk.variant.variantcontext	HtsJDK
VariantContext .Validation	Returns the enum constant of this type with the specified name.	Class	htsjdk.variant.variantcontext	HtsJDK
VariantContextBuilder	Builder class for VariantContext.	Class	htsjdk.variant.variantcontext	HtsJDK
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.	Class	htsjdk.variant.variantcontext	HtsJDK
VariantContextFilter	API for filtering VariantContextsAuthor:Yossi Farjoun	Interface	htsjdk.variant.variantcontext.filter	HtsJDK
VariantContextUtils		Class	htsjdk.variant.variantcontext	HtsJDK
VariantContextUtils .JexlVCMatchExp		Class	htsjdk.variant.variantcontext	HtsJDK
VariantContextWriter	this class writes VCF filesattempt to close the VCF file	Interface	htsjdk.variant.variantcontext.writer	HtsJDK
VariantContextWriterBuilder	Provides methods for creating VariantContextWriters using the Builder pattern.	Class	htsjdk.variant.variantcontext.writer	HtsJDK
VariantContextWriterBuilder .OutputType	Returns the enum constant of this type with the specified name.	Class	htsjdk.variant.variantcontext.writer	HtsJDK
VariantContextWriterFactory	Factory methods to create VariantContext writersSince:5/12Author:depristo	Class	htsjdk.variant.variantcontext.writer	HtsJDK

Search Java Classes and Packages