Package org.snpeff.vcf
Enum Class EffFormatVersion
- All Implemented Interfaces:
Serializable
,Comparable<EffFormatVersion>
,Constable
VcfFields in SnpEff version 2.X have a different format than 3.X
As of version 4.1 we switch to a standard annotation format
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Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
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Enum Constant Summary
Enum Constants -
Field Summary
Fields -
Method Summary
Modifier and TypeMethodDescriptionGet INF field name for corresponding formatboolean
isAnn()
Is this an 'ANN' format?boolean
isEff()
Id this an 'EFF' format?static boolean
Is this one of the VCF INFO keys?boolean
Is this format fully specified? I.e.Multiple effect separatorMultiple effect separator: Split regexstatic EffFormatVersion
Returns the enum constant of this class with the specified name.static EffFormatVersion[]
values()
Returns an array containing the constants of this enum class, in the order they are declared.VCF header for each format type
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Enum Constant Details
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FORMAT_EFF
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FORMAT_EFF_2
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FORMAT_EFF_3
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FORMAT_EFF_4
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FORMAT_ANN
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FORMAT_ANN_1
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Field Details
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DEFAULT_FORMAT_VERSION
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VCF_INFO_EFF_NAME
- See Also:
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VCF_INFO_ANN_NAME
- See Also:
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VCF_INFO_ANN_NAMES
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EFFECT_TYPE_SEPARATOR
- See Also:
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EFFECT_TYPE_SEPARATOR_OLD
- See Also:
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vcfInfoNames
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Method Details
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values
Returns an array containing the constants of this enum class, in the order they are declared.- Returns:
- an array containing the constants of this enum class, in the order they are declared
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valueOf
Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (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 class has no constant with the specified nameNullPointerException
- if the argument is null
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isEffectVcfInfoField
Is this one of the VCF INFO keys? -
infoFieldName
Get INF field name for corresponding format -
isAnn
public boolean isAnn()Is this an 'ANN' format? -
isEff
public boolean isEff()Id this an 'EFF' format? -
isFullVersion
public boolean isFullVersion()Is this format fully specified? I.e. does it have version number? -
separator
Multiple effect separator -
separatorSplit
Multiple effect separator: Split regex -
vcfHeader
VCF header for each format type
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