Uses of Class org.snpeff.interval.Variant (SnpEff 5.2 API)

Packages that use Variant

Package

Description

org.snpeff.align

org.snpeff.fileIterator

org.snpeff.interval

org.snpeff.interval.codonChange

org.snpeff.snpEffect

org.snpeff.stats

org.snpeff.vcf

Uses of Variant in org.snpeff.align

Methods in org.snpeff.align that return Variant

Modifier and Type

Method

Description

Variant

VariantRealign.getVariantRealigned()

Constructors in org.snpeff.align with parameters of type Variant

Modifier

Constructor

Description

VariantRealign(Variant variant)
Uses of Variant in org.snpeff.fileIterator

Methods in org.snpeff.fileIterator that return Variant

Modifier and Type

Method

Description

Variant

VariantTxtFileIterator.next()

protected Variant

BedFileIterator.readNext()

protected Variant

BigBedFileIterator.readNext()

protected Variant

VariantTxtFileIterator.readNext()
Uses of Variant in org.snpeff.interval

Subclasses of Variant in org.snpeff.interval

Modifier and Type

Class

Description

class

VariantBnd

A 'BND' variant (i.e.

class

VariantNonRef

A variant respect to non-reference (e.g.

class

VariantWithScore

A variant that has a numeric score.

Fields in org.snpeff.interval declared as Variant

Modifier and Type

Field

Description

static final Variant

Variant.NO_VARIANT

Methods in org.snpeff.interval that return Variant

Modifier and Type

Method

Description

Variant

Variant.clone()

Variant

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 + InDel

Variant

VariantNonRef.getVariantRef()

Variant

Variant.realignLeft()

Create a new variant realigning it towards the leftmost position

Variant

VariantBnd.realignLeft()

Variant

VariantNonRef.realignLeft()

Variant

Variant.reverse()

Reverse variant (e.g.

Methods in org.snpeff.interval that return types with arguments of type Variant

Modifier and Type

Method

Description

static List<Variant>

Variant.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 Variant

Modifier and Type

Method

Description

Exon

Exon.apply(Variant variant)

Apply variant to exon WARNING: There might be conditions which change the exon type (e.g.

IntervalAndSubIntervals<T>

IntervalAndSubIntervals.apply(Variant variant)

Apply a variant.

Intron

Intron.apply(Variant variant)

Marker

Marker.apply(Variant variant)

Apply a variant to a marker.

MarkerSeq

MarkerSeq.apply(Variant variant)

Apply variant

Transcript

Transcript.apply(Variant variant)

Create a new transcript after applying changes in variant

protected Marker

Marker.applyDel(Variant variant)

Apply a Variant to a marker.

protected void

MarkerSeq.applyDel(Variant variant, MarkerSeq markerSeq)

Apply a change type deletion (update sequence)

protected Marker

Marker.applyDup(Variant variant)

Apply a Variant to a marker.

protected void

MarkerSeq.applyDup(Variant variant, MarkerSeq markerSeq)

Apply a change type duplication (update sequence)

protected Marker

Marker.applyIns(Variant variant)

Apply a Variant to a marker.

protected void

MarkerSeq.applyIns(Variant variant, MarkerSeq markerSeq)

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

MarkerSeq.applyMnp(Variant variant, MarkerSeq markerSeq)

Apply a change type MNP (update sequence)

protected void

MarkerSeq.applySnp(Variant variant, MarkerSeq markerSeq)

Apply a change type SNP (update sequence)

int

Downstream.distanceToTr(Variant variant)

Distance to transcript

int

Upstream.distanceToTr(Variant variant)

Distance to transcript

ErrorWarningType

Exon.sanityCheck(Variant variant)

Check that the base in the exon corresponds with the one in the SNP

ErrorWarningType

Transcript.sanityCheck(Variant variant)

Perfom some baseic chekcs, return error type, if any

void

VariantNonRef.setVariantRef(Variant variantRef)

boolean

Marker.shouldApply(Variant variant)

True if the variant should be applied to the marker

boolean

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' class

boolean

Gene.variantEffect(Variant variant, VariantEffects variantEffects)

Get some details about the effect on this gene

boolean

Intron.variantEffect(Variant variant, VariantEffects variantEffects)

boolean

Marker.variantEffect(Variant variant, VariantEffects variantEffects)

Calculate the effect of this variant

boolean

MicroRnaBindingSite.variantEffect(Variant variant, VariantEffects changeEffects)

boolean

Motif.variantEffect(Variant variant, VariantEffects variantEffects)

Calculate the effect of this variant

boolean

NextProt.variantEffect(Variant variant, VariantEffects variantEffects)

boolean

ProteinInteractionLocus.variantEffect(Variant variant, VariantEffects variantEffects)

Calculate the effect of this variant

boolean

ProteinProteinInteractionLocus.variantEffect(Variant variant, VariantEffects variantEffects)

Calculate the effect of this variant

boolean

Regulation.variantEffect(Variant variant, VariantEffects variantEffects)

Calculate the effect of this variant

boolean

SpliceSite.variantEffect(Variant variant, VariantEffects variantEffects)

boolean

Transcript.variantEffect(Variant variant, VariantEffects variantEffects)

Get some details about the effect on this transcript

boolean

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 annotations

boolean

Marker.variantEffectNonRef(Variant variant, VariantEffects variantEffects)

Calculate the effect of this variant

Constructors in org.snpeff.interval with parameters of type Variant

Modifier

Constructor

Description

VariantNonRef(Variant variant, Variant variantRef)
Uses of Variant in org.snpeff.interval.codonChange

Methods in org.snpeff.interval.codonChange with parameters of type Variant

Modifier and Type

Method

Description

static CodonChange

CodonChange.factory(Variant variant, Transcript transcript, VariantEffects variantEffects)

Create a specific codon change for a variant

Constructors in org.snpeff.interval.codonChange with parameters of type Variant

Modifier

Constructor

Description

protected

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 Variant

Modifier and Type

Field

Description

protected Variant

Hgvs.variant

protected Variant

VariantEffect.variant

Methods in org.snpeff.snpEffect that return Variant

Modifier and Type

Method

Description

Variant

VariantEffect.getVariant()

Methods in org.snpeff.snpEffect with parameters of type Variant

Modifier and Type

Method

Description

void

VariantEffects.add(Variant variant, Marker marker, EffectType effectType, String message)

Add an effect

void

VariantEffects.add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message)

Add an effect

void

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)

String

EffectType.toSequenceOntology(EffFormatVersion formatVersion, Variant variant)

VariantEffects

SnpEffectPredictor.variantEffect(Variant variant)

Predict the effect of a variant

protected void

SnpEffectPredictor.variantEffect(Variant variant, VariantEffects variantEffects, Markers intersects)

Calculate variant effect for each marker in 'intersect'

Constructors in org.snpeff.snpEffect with parameters of type Variant

Modifier

Constructor

Description

VariantEffect(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

Modifier and Type

Method

Description

void

VariantStats.sample(Variant variant)

Use this sample to perform statistics
Uses of Variant in org.snpeff.vcf

Subclasses of Variant in org.snpeff.vcf

Modifier and Type

Class

Description

class

VariantVcfEntry

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 Variant

Modifier and Type

Field

Description

protected LinkedList<Variant>

VcfEntry.variants

Methods in org.snpeff.vcf that return types with arguments of type Variant

Modifier and Type

Method

Description

List<Variant>

VcfEntry.variants()

Create a list of variants from this VcfEntry

Methods in org.snpeff.vcf with parameters of type Variant

Modifier and Type

Method

Description

String

VcfEntry.getInfo(String key, Variant var)

Get an INFO field matching a variant

Constructors in org.snpeff.vcf with parameters of type Variant

Modifier

Constructor

Description

VariantVcfEntry(Variant variant, VcfEntry vcfEntry)

Uses of Classorg.snpeff.interval.Variant

Uses of Variant in org.snpeff.align

Uses of Variant in org.snpeff.fileIterator

Uses of Variant in org.snpeff.interval

Uses of Variant in org.snpeff.interval.codonChange

Uses of Variant in org.snpeff.snpEffect

Uses of Variant in org.snpeff.stats

Uses of Variant in org.snpeff.vcf

Uses of Class
org.snpeff.interval.Variant