htsjdk.variant.variantcontext

Enum VariantContext.Type

java.lang.Object

java.lang.Enum<VariantContext.Type>

htsjdk.variant.variantcontext.VariantContext.Type

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<VariantContext.Type>

Enclosing class:

VariantContext

public static enum VariantContext.Type
extends java.lang.Enum<VariantContext.Type>

See Also:

NCBI Handbook

Format:

• dbSNP variation class
• Rules for assigning allele classes
• Sample allele definition

Supported Types

• Single Nucleotide Polymorphisms (SNPs)a
• Strictly defined as single base substitutions involving A, T, C, or G.
• A/T

• Deletion/Insertion Polymorphisms (DIPs)
• Designated using the full sequence of the insertion as one allele, and either a fully defined string for the variant allele or a '-' character to specify the deleted allele. This class will be assigned to a variation if the variation alleles are of different lengths or if one of the alleles is deleted ('-').
• T/-/CCTA/G

• No-variation
• Reports may be submitted for segments of sequence that are assayed and determined to be invariant in the sample.
• (NoVariation)

• Mixed
• Mix of other classes

Also supports NO_VARIATION type, used to indicate that the site isn't polymorphic in the population

Not currently supported:

• Heterozygous sequence
• The term heterozygous is used to specify a region detected by certain methods that do not resolve the polymorphism into a specific sequence motif. In these cases, a unique flanking sequence must be provided to define a sequence context for the variation.
• (heterozygous)

• Microsatellite or short tandem repeat (STR)
• Alleles are designated by providing the repeat motif and the copy number for each allele. Expansion of the allele repeat motif designated in dbSNP into full-length sequence will be only an approximation of the true genomic sequence because many microsatellite markers are not fully sequenced and are resolved as size variants only.
• (CAC)8/9/10/11

• Named variant
• Applies to insertion/deletion polymorphisms of longer sequence features, such as retroposon dimorphism for Alu or line elements. These variations frequently include a deletion '-' indicator for the absent allele.
• (alu) / -

• Multi-Nucleotide Polymorphism (MNP)
• Assigned to variations that are multi-base variations of a single, common length
• GGA/AGT

Enum Constant Summary

Enum Constants

Enum Constant and Description
INDEL
MIXED
MNP
NO_VARIATION
SNP
SYMBOLIC

Method Summary

Modifier and Type	Method and Description
static VariantContext.Type	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static VariantContext.Type[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

NO_VARIATION

public static final VariantContext.Type NO_VARIATION

SNP

public static final VariantContext.Type SNP

MNP

public static final VariantContext.Type MNP

INDEL

public static final VariantContext.Type INDEL

SYMBOLIC

public static final VariantContext.Type SYMBOLIC

MIXED

public static final VariantContext.Type MIXED

Method Detail

values

public static VariantContext.Type[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (VariantContext.Type c : VariantContext.Type.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static VariantContext.Type valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null