Uses of Class
org.snpeff.vcf.EffFormatVersion
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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)
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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 stringstatic EffectType
EffectType. parse(EffFormatVersion formatVersion, java.lang.String str)
Parse a string to an EffectTypejava.lang.String
EffectType. toSequenceOntology(EffFormatVersion formatVersion, Variant variant)
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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)
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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 versionprotected EffFormatVersion
VcfEffect. formatVersion(java.lang.String effectString)
Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-versionEffFormatVersion
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 effectsstatic java.lang.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 EffFormatVersion Constructor Description VcfEffect(java.lang.String effectString, EffFormatVersion formatVersion)
Constructor: Force format versionVcfEffect(VariantEffect variantEffect, EffFormatVersion formatVersion)
VcfEffect(VariantEffect variantEffect, EffFormatVersion formatVersion, boolean useSequenceOntology, boolean useFirstEffect)
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