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 TypeMethodDescriptionvoidVcfOutputFormatter.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 EffectTypeEffectType.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 TypeMethodDescriptionvoidSnpEffCmdEff.setFormatVersion(EffFormatVersion formatVersion) -
Uses of EffFormatVersion in org.snpeff.snpEffect.testCases.integration
Methods in org.snpeff.snpEffect.testCases.integration with parameters of type EffFormatVersion -
Uses of EffFormatVersion in org.snpeff.snpEffect.testCases.unity
Methods in org.snpeff.snpEffect.testCases.unity that return EffFormatVersionModifier and TypeMethodDescriptionprotected EffFormatVersionTestCasesBase.formatVersion(String vcfFileName) Get file's format version -
Uses of EffFormatVersion in org.snpeff.vcf
Fields in org.snpeff.vcf declared as EffFormatVersionModifier and TypeFieldDescriptionstatic final EffFormatVersionEffFormatVersion.DEFAULT_FORMAT_VERSIONMethods in org.snpeff.vcf that return EffFormatVersionModifier and TypeMethodDescriptionVcfEffect.formatVersion()Guess effect format versionprotected EffFormatVersionVcfEffect.formatVersion(String effectString) Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-versionVcfEffect.getFormatVersion()static EffFormatVersionReturns 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 StringVcfEffect.infoFieldName(EffFormatVersion formatVersion) Get info field name based on format versionvoidVcfEffect.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)