Uses of Class
org.snpeff.snpEffect.VariantEffect
-
Packages that use VariantEffect Package Description org.snpeff.filter org.snpeff.interval org.snpeff.interval.codonChange org.snpeff.outputFormatter org.snpeff.snpEffect org.snpeff.stats org.snpeff.vcf -
-
Uses of VariantEffect in org.snpeff.filter
Methods in org.snpeff.filter with parameters of type VariantEffect Modifier and Type Method Description boolean
VariantEffectFilter. filter(VariantEffect variantEffect)
Filter a sequence change -
Uses of VariantEffect in org.snpeff.interval
Methods in org.snpeff.interval with parameters of type VariantEffect Modifier and Type Method Description java.lang.String
Marker. idChain(java.lang.String separatorBetween, java.lang.String separatorWithin, boolean useGeneId, VariantEffect varEff)
A list of all IDs and parent IDs until chromosome -
Uses of VariantEffect in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange that return VariantEffect Modifier and Type Method Description protected VariantEffect
CodonChange. effect(Marker marker, EffectType effectType, boolean allowReplace)
Calculate variant effectprotected VariantEffect
CodonChange. effectNoCodon(Marker marker, EffectType effectType)
protected VariantEffect
CodonChange. effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact)
-
Uses of VariantEffect in org.snpeff.outputFormatter
Methods in org.snpeff.outputFormatter with parameters of type VariantEffect Modifier and Type Method Description void
OutputFormatter. add(VariantEffect variantEffect)
Add effects to list -
Uses of VariantEffect in org.snpeff.snpEffect
Subclasses of VariantEffect in org.snpeff.snpEffect Modifier and Type Class Description class
VariantEffectFusion
Effect of a structural variant (fusion) affecting two genesclass
VariantEffectStructural
Effect of a structural variant affecting multiple genesFields in org.snpeff.snpEffect declared as VariantEffect Modifier and Type Field Description protected VariantEffect
Hgvs. variantEffect
Methods in org.snpeff.snpEffect that return VariantEffect Modifier and Type Method Description VariantEffect
VariantEffect. clone()
VariantEffect
VariantEffects. get()
Get (or create) the latest ChangeEffectVariantEffect
VariantEffects. get(int index)
Methods in org.snpeff.snpEffect that return types with arguments of type VariantEffect Modifier and Type Method Description java.util.List<VariantEffect>
VariantEffectStructural. fusions()
Is there another 'fusion' effect?java.util.Iterator<VariantEffect>
VariantEffects. iterator()
Methods in org.snpeff.snpEffect with parameters of type VariantEffect Modifier and Type Method Description void
VariantEffects. add(VariantEffect variantEffect)
Add an effectint
VariantEffect. compareTo(VariantEffect varEffOther)
protected boolean
LossOfFunction. isLof(VariantEffect variantEffect)
Is this single change a LOF? Criteria: 1) Core splice sites acceptors or donors (only CORE ones) 2) Stop gained (if this happens at the last part of the protein, we assume it has no effect) 3) Frame shiftsprotected boolean
LossOfFunction. isLofDeletion(VariantEffect variantEffect)
Is this deletion a LOF? Criteria: 1) First (coding) exon deleted 2) More than 50% of coding sequence deletedprotected boolean
LossOfFunction. isNmd(VariantEffect variantEffect)
Is this single change a LOF? Criteria: 1) Core splice sites acceptors or donors (only CORE ones) 2) Stop gained (if this happens at the last part of the protein, we assume it has no effect) 3) Frame shiftsConstructors in org.snpeff.snpEffect with parameters of type VariantEffect Constructor Description Hgvs(VariantEffect variantEffect)
HgvsDna(VariantEffect variantEffect)
HgvsProtein(VariantEffect variantEffect)
Constructor parameters in org.snpeff.snpEffect with type arguments of type VariantEffect Constructor Description LossOfFunction(Config config, java.util.Collection<VariantEffect> variantEffects)
-
Uses of VariantEffect in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type VariantEffect Modifier and Type Method Description void
GeneCountByTypeTable. sample(Gene gene, Transcript tr, java.lang.String type, VariantEffect variantEffect)
Sample thistuple to update statistics void
VariantEffectStats. sample(VariantEffect variantEffect)
-
Uses of VariantEffect in org.snpeff.vcf
Constructors in org.snpeff.vcf with parameters of type VariantEffect Constructor Description VcfEffect(VariantEffect variantEffect, EffFormatVersion formatVersion)
VcfEffect(VariantEffect variantEffect, EffFormatVersion formatVersion, boolean useSequenceOntology, boolean useFirstEffect)
-