Uses of Class
org.snpeff.vcf.EffFormatVersion

Packages that use EffFormatVersion

Package	Description
org.snpeff.outputFormatter
org.snpeff.snpEffect
org.snpeff.snpEffect.commandLine
org.snpeff.snpEffect.testCases.integration
org.snpeff.snpEffect.testCases.unity
org.snpeff.vcf

Uses of EffFormatVersion in org.snpeff.outputFormatter

Methods in org.snpeff.outputFormatter with parameters of type EffFormatVersion

Modifier and Type	Method	Description
void	VcfOutputFormatter.setFormatVersion(EffFormatVersion formatVersion)

Uses of EffFormatVersion in org.snpeff.snpEffect

Methods in org.snpeff.snpEffect with parameters of type EffFormatVersion

Modifier and Type	Method	Description
java.lang.String	VariantEffect.getEffectTypeString(boolean useSeqOntology, boolean useFirstEffect, EffFormatVersion formatVersion)	Get Effect Type as a string
static EffectType	EffectType.parse(EffFormatVersion formatVersion, java.lang.String str)	Parse a string to an EffectType
java.lang.String	EffectType.toSequenceOntology(EffFormatVersion formatVersion, Variant variant)

Uses of EffFormatVersion in org.snpeff.snpEffect.commandLine

Methods in org.snpeff.snpEffect.commandLine with parameters of type EffFormatVersion

Modifier and Type	Method	Description
void	SnpEffCmdEff.setFormatVersion(EffFormatVersion formatVersion)

Uses of EffFormatVersion in org.snpeff.snpEffect.testCases.integration

Methods in org.snpeff.snpEffect.testCases.integration with parameters of type EffFormatVersion

Modifier and Type	Method	Description
java.util.List<VcfEntry>	TestCasesIntegrationBase.snpEffect(java.lang.String genome, java.lang.String vcfFile, java.lang.String[] otherArgs, EffFormatVersion effFormatVersion)	Calculate snp effect for an input VCF file

Uses of EffFormatVersion in org.snpeff.snpEffect.testCases.unity

Methods in org.snpeff.snpEffect.testCases.unity that return EffFormatVersion

Modifier and Type	Method	Description
protected EffFormatVersion	TestCasesBase.formatVersion(java.lang.String vcfFileName)	Get file's format version

Uses of EffFormatVersion in org.snpeff.vcf

Fields in org.snpeff.vcf declared as EffFormatVersion

Modifier and Type	Field	Description
static EffFormatVersion	EffFormatVersion.DEFAULT_FORMAT_VERSION

Methods in org.snpeff.vcf that return EffFormatVersion

Modifier and Type	Method	Description
EffFormatVersion	VcfEffect.formatVersion()	Guess effect format version
protected EffFormatVersion	VcfEffect.formatVersion(java.lang.String effectString)	Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-version
EffFormatVersion	VcfEffect.getFormatVersion()
static EffFormatVersion	EffFormatVersion.valueOf(java.lang.String name)	Returns the enum constant of this type with the specified name.
static EffFormatVersion[]	EffFormatVersion.values()	Returns an array containing the constants of this enum type, in the order they are declared.

Methods in org.snpeff.vcf with parameters of type EffFormatVersion

Modifier and Type	Method	Description
java.util.List<VcfEffect>	VcfEntry.getVcfEffects(EffFormatVersion formatVersion)	Parse 'EFF' info field and get a list of effects
static java.lang.String	VcfEffect.infoFieldName(EffFormatVersion formatVersion)	Get info field name based on format version
void	VcfEffect.setFormatVersion(EffFormatVersion formatVersion)

Constructors in org.snpeff.vcf with parameters of type EffFormatVersion

Constructor	Description
VcfEffect(java.lang.String effectString, EffFormatVersion formatVersion)	Constructor: Force format version
VcfEffect(VariantEffect variantEffect, EffFormatVersion formatVersion)
VcfEffect(VariantEffect variantEffect, EffFormatVersion formatVersion, boolean useSequenceOntology, boolean useFirstEffect)