Uses of Enum Class
org.snpeff.vcf.EffFormatVersion
Packages that use EffFormatVersion
Package
Description
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Uses of EffFormatVersion in org.snpeff.outputFormatter
Methods in org.snpeff.outputFormatter with parameters of type EffFormatVersionModifier and TypeMethodDescriptionvoid
VcfOutputFormatter.setFormatVersion
(EffFormatVersion formatVersion) -
Uses of EffFormatVersion in org.snpeff.snpEffect
Methods in org.snpeff.snpEffect with parameters of type EffFormatVersionModifier and TypeMethodDescriptionVariantEffect.getEffectTypeString
(boolean useSeqOntology, boolean useFirstEffect, EffFormatVersion formatVersion) Get Effect Type as a stringstatic EffectType
EffectType.parse
(EffFormatVersion formatVersion, String str) Parse a string to an EffectTypeEffectType.toSequenceOntology
(EffFormatVersion formatVersion, Variant variant) -
Uses of EffFormatVersion in org.snpeff.snpEffect.commandLine
Methods in org.snpeff.snpEffect.commandLine with parameters of type EffFormatVersionModifier and TypeMethodDescriptionvoid
SnpEffCmdEff.setFormatVersion
(EffFormatVersion formatVersion) -
Uses of EffFormatVersion in org.snpeff.vcf
Fields in org.snpeff.vcf declared as EffFormatVersionModifier and TypeFieldDescriptionstatic final EffFormatVersion
EffFormatVersion.DEFAULT_FORMAT_VERSION
Methods in org.snpeff.vcf that return EffFormatVersionModifier and TypeMethodDescriptionVcfEffect.formatVersion()
Guess effect format versionprotected EffFormatVersion
VcfEffect.formatVersion
(String effectString) Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-versionVcfEffect.getFormatVersion()
static EffFormatVersion
Returns the enum constant of this class with the specified name.static EffFormatVersion[]
EffFormatVersion.values()
Returns an array containing the constants of this enum class, in the order they are declared.Methods in org.snpeff.vcf with parameters of type EffFormatVersionModifier and TypeMethodDescriptionVcfEntry.getVcfEffects
(EffFormatVersion formatVersion) Parse 'EFF' info field and get a list of effectsstatic String
VcfEffect.infoFieldName
(EffFormatVersion formatVersion) Get info field name based on format versionvoid
VcfEffect.setFormatVersion
(EffFormatVersion formatVersion) Constructors in org.snpeff.vcf with parameters of type EffFormatVersionModifierConstructorDescriptionVcfEffect
(String effectString, EffFormatVersion formatVersion) Constructor: Force format versionVcfEffect
(VariantEffect variantEffect, EffFormatVersion formatVersion) VcfEffect
(VariantEffect variantEffect, EffFormatVersion formatVersion, boolean useSequenceOntology, boolean useFirstEffect)