Uses of Class
org.snpeff.interval.Variant
Packages that use Variant
Package
Description
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Uses of Variant in org.snpeff.align
Methods in org.snpeff.align that return VariantConstructors in org.snpeff.align with parameters of type Variant -
Uses of Variant in org.snpeff.fileIterator
Methods in org.snpeff.fileIterator that return Variant -
Uses of Variant in org.snpeff.interval
Subclasses of Variant in org.snpeff.intervalModifier and TypeClassDescriptionclass
A 'BND' variant (i.e.class
A variant respect to non-reference (e.g.class
A variant that has a numeric score.Fields in org.snpeff.interval declared as VariantMethods in org.snpeff.interval that return VariantModifier and TypeMethodDescriptionVariant.clone()
Variant.cloneShallow()
Variant[]
Variant.decompose()
Decompose a variant into basic constituents At the moment this only makes sense for MIXED variants which are decomposed into two variants: MNP + InDelVariantNonRef.getVariantRef()
Variant.realignLeft()
Create a new variant realigning it towards the leftmost positionVariantBnd.realignLeft()
VariantNonRef.realignLeft()
Variant.reverse()
Reverse variant (e.g.Methods in org.snpeff.interval that return types with arguments of type VariantModifier and TypeMethodDescriptionVariant.factory
(Chromosome chromo, int start, String ref, String altStr, String id, boolean expand) Create variants from ALT (which can be multiple values)Methods in org.snpeff.interval with parameters of type VariantModifier and TypeMethodDescriptionApply variant to exon WARNING: There might be conditions which change the exon type (e.g.Apply a variant.Apply a variant to a marker.Apply variantCreate a new transcript after applying changes in variantprotected Marker
Apply a Variant to a marker.protected void
Apply a change type deletion (update sequence)protected Marker
Apply a Variant to a marker.protected void
Apply a change type duplication (update sequence)protected Marker
Apply a Variant to a marker.protected void
Apply a change type insertion (update sequence)protected Marker
Marker.applyMixed
(Variant variant) Apply a mixed variant Note: MIXED variant is interpreted as "MNP + InDel"protected void
Apply a change type MNP (update sequence)protected void
Apply a change type SNP (update sequence)int
Downstream.distanceToTr
(Variant variant) Distance to transcriptint
Upstream.distanceToTr
(Variant variant) Distance to transcriptExon.sanityCheck
(Variant variant) Check that the base in the exon corresponds with the one in the SNPTranscript.sanityCheck
(Variant variant) Perfom some baseic chekcs, return error type, if anyvoid
VariantNonRef.setVariantRef
(Variant variantRef) boolean
Marker.shouldApply
(Variant variant) True if the variant should be applied to the markerboolean
Custom.variantEffect
(Variant variant, VariantEffects changeEffecs) boolean
Downstream.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Exon.variantEffect
(Variant variant, VariantEffects variantEffects) Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' classboolean
Gene.variantEffect
(Variant variant, VariantEffects variantEffects) Get some details about the effect on this geneboolean
Intron.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Marker.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
MicroRnaBindingSite.variantEffect
(Variant variant, VariantEffects changeEffects) boolean
Motif.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
NextProt.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
ProteinInteractionLocus.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
ProteinProteinInteractionLocus.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
Regulation.variantEffect
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantboolean
SpliceSite.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Transcript.variantEffect
(Variant variant, VariantEffects variantEffects) Get some details about the effect on this transcriptboolean
Upstream.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Utr3prime.variantEffect
(Variant variant, VariantEffects variantEffects) boolean
Utr5prime.variantEffect
(Variant variant, VariantEffects variantEffects) protected void
Gene.variantEffectGene
(Variant variant, VariantEffects variantEffects) Add gene-specific annotationsboolean
Marker.variantEffectNonRef
(Variant variant, VariantEffects variantEffects) Calculate the effect of this variantConstructors in org.snpeff.interval with parameters of type Variant -
Uses of Variant in org.snpeff.interval.codonChange
Methods in org.snpeff.interval.codonChange with parameters of type VariantModifier and TypeMethodDescriptionstatic CodonChange
CodonChange.factory
(Variant variant, Transcript transcript, VariantEffects variantEffects) Create a specific codon change for a variantConstructors in org.snpeff.interval.codonChange with parameters of type VariantModifierConstructorDescriptionprotected
CodonChange
(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeDel
(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeDup
(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeIns
(Variant variant, Transcript transcript, VariantEffects changeEffects) CodonChangeInterval
(Variant variant, Transcript transcript, VariantEffects varEffects) CodonChangeInv
(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeMixed
(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeMnp
(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeSnp
(Variant variant, Transcript transcript, VariantEffects variantEffects) CodonChangeStructural
(Variant variant, Transcript transcript, VariantEffects variantEffects) -
Uses of Variant in org.snpeff.snpEffect
Fields in org.snpeff.snpEffect declared as VariantModifier and TypeFieldDescriptionprotected Variant
Hgvs.variant
protected Variant
VariantEffect.variant
Methods in org.snpeff.snpEffect that return VariantMethods in org.snpeff.snpEffect with parameters of type VariantModifier and TypeMethodDescriptionvoid
VariantEffects.add
(Variant variant, Marker marker, EffectType effectType, String message) Add an effectvoid
VariantEffects.add
(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) Add an effectvoid
VariantEffects.addEffectType
(Variant variant, Marker marker, EffectType effectType) Add: If possible, only add an effect type (otherwise add the full effect)void
VariantEffects.addErrorWarning
(Variant variant, ErrorWarningType errwarn) EffectType.toSequenceOntology
(EffFormatVersion formatVersion, Variant variant) SnpEffectPredictor.variantEffect
(Variant variant) Predict the effect of a variantprotected void
SnpEffectPredictor.variantEffect
(Variant variant, VariantEffects variantEffects, Markers intersects) Calculate variant effect for each marker in 'intersect'void
ProteinFastaWriter.write
(Variant var, VariantEffects variantEffects) Append ALT protein sequence to fasta protein fileConstructors in org.snpeff.snpEffect with parameters of type VariantModifierConstructorDescriptionVariantEffect
(Variant variant) VariantEffect
(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String codonsOld, String codonsNew, int codonNum, int codonIndex, int cDnaPos) VariantEffectFusion
(Variant variant, Marker mLeft, Marker mRight) VariantEffectStructural
(Variant variant) VariantEffectStructural
(Variant variant, Markers intersects) -
Uses of Variant in org.snpeff.stats
Methods in org.snpeff.stats with parameters of type Variant -
Uses of Variant in org.snpeff.vcf
Subclasses of Variant in org.snpeff.vcfModifier and TypeClassDescriptionclass
Variant + VcfEntry This is used to 'outer-join' a VcfEntry into all its constituent variants.Fields in org.snpeff.vcf with type parameters of type VariantMethods in org.snpeff.vcf that return types with arguments of type VariantModifier and TypeMethodDescriptionVcfEntry.variants()
Create a list of variants from this VcfEntryMethods in org.snpeff.vcf with parameters of type VariantModifier and TypeMethodDescriptionGet an INFO field matching a variantConstructors in org.snpeff.vcf with parameters of type Variant