| Interface | Description |
|---|---|
| LazyGenotypesContext.LazyParser |
Simple lazy parser interface.
|
| Class | Description |
|---|---|
| Allele |
Immutable representation of an allele
Types of alleles:
Ref: a t C g a // C is the reference base
: a t G g a // C base is a G in some individuals
: a t - g a // C base is deleted w.r.t.
|
| 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 |
Class VariantContext
== High-level overview ==
The VariantContext object is a single general class system for representing genetic variation data composed of:
* Allele: representing single genetic haplotypes (A, T, ATC, -) (note that null alleles are used here for illustration; see the Allele class for how to represent indels)
* Genotype: an assignment of alleles for each chromosome of a single named sample at a particular locus
* VariantContext: an abstract class holding all segregating alleles at a locus as well as genotypes
for multiple individuals containing alleles at that locus
The class system works by defining segregating alleles, creating a variant context representing the segregating
information at a locus, and potentially creating and associating genotypes with individuals in the context.
|
| VariantContextBuilder |
Builder class for VariantContext
Some basic assumptions here:
1 -- data isn't protectively copied.
|
| 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 |
see: http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch5&rendertype=table&id=ch5.ch5_t3
Format:
dbSNP variation class
Rules for assigning allele classes
Sample allele definition
Single Nucleotide Polymorphisms (SNPs)a
Strictly defined as single base substitutions involving A, T, C, or G.
|
| VariantContext.Validation |