| Interface | Description |
|---|---|
| LazyGenotypesContext.LazyParser |
Simple lazy parser interface.
|
| 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.
|
| GenotypeLikelihoods | |
| GenotypeLikelihoods.GenotypeLikelihoodsAllelePair | |
| GenotypesContext |
Represents an ordered collection of Genotype objects
|
| LazyGenotypesContext |
Lazy-loading GenotypesContext.
|
| 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
|
| 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
|
| Enum | Description |
|---|---|
| GenotypeType |
Summary types for Genotype objects
|
| VariantContext.Type | |
| VariantContext.Validation |