Package htsjdk.variant.variantcontext
Enum VariantContext.Type
- java.lang.Object
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- java.lang.Enum<VariantContext.Type>
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- htsjdk.variant.variantcontext.VariantContext.Type
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- All Implemented Interfaces:
Serializable
,Comparable<VariantContext.Type>
- Enclosing class:
- VariantContext
public static enum VariantContext.Type extends 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
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
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static VariantContext.Type
valueOf(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.
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Enum Constant Detail
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NO_VARIATION
public static final VariantContext.Type NO_VARIATION
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SNP
public static final VariantContext.Type SNP
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MNP
public static final VariantContext.Type MNP
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INDEL
public static final VariantContext.Type INDEL
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SYMBOLIC
public static final VariantContext.Type SYMBOLIC
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MIXED
public static final VariantContext.Type MIXED
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Method Detail
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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
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valueOf
public static VariantContext.Type valueOf(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:
IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null
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