Package org.snpeff.vcf
Enum EffFormatVersion
- java.lang.Object
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- java.lang.Enum<EffFormatVersion>
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- org.snpeff.vcf.EffFormatVersion
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Comparable<EffFormatVersion>
public enum EffFormatVersion extends java.lang.Enum<EffFormatVersion>
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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Enum Constant Summary
Enum Constants Enum Constant Description FORMAT_ANN
FORMAT_ANN_1
FORMAT_EFF
FORMAT_EFF_2
FORMAT_EFF_3
FORMAT_EFF_4
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Field Summary
Fields Modifier and Type Field Description static EffFormatVersion
DEFAULT_FORMAT_VERSION
static java.lang.String
EFFECT_TYPE_SEPARATOR
static java.lang.String
EFFECT_TYPE_SEPARATOR_OLD
static java.lang.String
VCF_INFO_ANN_NAME
static java.lang.String[]
VCF_INFO_ANN_NAMES
static java.lang.String
VCF_INFO_EFF_NAME
protected static java.util.Set<java.lang.String>
vcfInfoNames
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
infoFieldName()
Get INF field name for corresponding formatboolean
isAnn()
Is this an 'ANN' format?boolean
isEff()
Id this an 'EFF' format?static boolean
isEffectVcfInfoField(java.lang.String key)
Is this one of the VCF INFO keys?boolean
isFullVersion()
Is this format fully specified? I.e.java.lang.String
separator()
Multiple effect separatorjava.lang.String
separatorSplit()
Multiple effect separator: Split regexstatic EffFormatVersion
valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.static EffFormatVersion[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.java.lang.String
vcfHeader()
VCF header for each format type
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Enum Constant Detail
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FORMAT_EFF
public static final EffFormatVersion FORMAT_EFF
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FORMAT_EFF_2
public static final EffFormatVersion FORMAT_EFF_2
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FORMAT_EFF_3
public static final EffFormatVersion FORMAT_EFF_3
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FORMAT_EFF_4
public static final EffFormatVersion FORMAT_EFF_4
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FORMAT_ANN
public static final EffFormatVersion FORMAT_ANN
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FORMAT_ANN_1
public static final EffFormatVersion FORMAT_ANN_1
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Field Detail
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DEFAULT_FORMAT_VERSION
public static final EffFormatVersion DEFAULT_FORMAT_VERSION
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VCF_INFO_EFF_NAME
public static final java.lang.String VCF_INFO_EFF_NAME
- See Also:
- Constant Field Values
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VCF_INFO_ANN_NAME
public static final java.lang.String VCF_INFO_ANN_NAME
- See Also:
- Constant Field Values
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VCF_INFO_ANN_NAMES
public static final java.lang.String[] VCF_INFO_ANN_NAMES
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EFFECT_TYPE_SEPARATOR
public static final java.lang.String EFFECT_TYPE_SEPARATOR
- See Also:
- Constant Field Values
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EFFECT_TYPE_SEPARATOR_OLD
public static final java.lang.String EFFECT_TYPE_SEPARATOR_OLD
- See Also:
- Constant Field Values
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vcfInfoNames
protected static java.util.Set<java.lang.String> vcfInfoNames
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Method Detail
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values
public static EffFormatVersion[] 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 (EffFormatVersion c : EffFormatVersion.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 EffFormatVersion 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 namejava.lang.NullPointerException
- if the argument is null
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isEffectVcfInfoField
public static boolean isEffectVcfInfoField(java.lang.String key)
Is this one of the VCF INFO keys?
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infoFieldName
public java.lang.String infoFieldName()
Get INF field name for corresponding format
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isAnn
public boolean isAnn()
Is this an 'ANN' format?
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isEff
public boolean isEff()
Id this an 'EFF' format?
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isFullVersion
public boolean isFullVersion()
Is this format fully specified? I.e. does it have version number?
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separator
public java.lang.String separator()
Multiple effect separator
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separatorSplit
public java.lang.String separatorSplit()
Multiple effect separator: Split regex
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vcfHeader
public java.lang.String vcfHeader()
VCF header for each format type
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