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 effect
protected 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 genes
class	VariantEffectStructural	Effect of a structural variant affecting multiple genes

Fields 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 ChangeEffect
VariantEffect	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 effect
int	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 shifts
protected boolean	LossOfFunction.isLofDeletion(VariantEffect variantEffect)	Is this deletion a LOF? Criteria: 1) First (coding) exon deleted 2) More than 50% of coding sequence deleted
protected 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 shifts

Constructors 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 this tuple 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)