Uses of Class
org.snpeff.interval.Variant

Packages that use Variant

Package	Description
org.snpeff.align
org.snpeff.fileIterator
org.snpeff.interval
org.snpeff.interval.codonChange
org.snpeff.snpEffect
org.snpeff.snpEffect.testCases.integration
org.snpeff.snpEffect.testCases.unity
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

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 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 java.util.List<Variant>	Variant.factory(Chromosome chromo, int start, java.lang.String ref, java.lang.String altStr, java.lang.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

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

Constructor	Description
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, java.lang.String message)	Add an effect
void	VariantEffects.add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.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)
java.lang.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

Constructor	Description
VariantEffect(Variant variant)
VariantEffect(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.String codonsOld, java.lang.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.snpEffect.testCases.integration

Methods in org.snpeff.snpEffect.testCases.integration that return types with arguments of type Variant

Modifier and Type	Method	Description
java.util.List<Variant>	CompareEffects.parseSnpEffectFile(java.lang.String variantFile)	Parse a variant file and return a list

Method parameters in org.snpeff.snpEffect.testCases.integration with type arguments of type Variant

Modifier and Type	Method	Description
void	CompareEffects.snpEffect(java.util.List<Variant> variantList, java.lang.String transcriptId, boolean useShort, boolean negate)	Calculate snp effect for a list of snps

Uses of Variant in org.snpeff.snpEffect.testCases.unity

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

Modifier and Type	Method	Description
void	TestCasesBase.checkApply(Variant variant, Variant.VariantType varType, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)	Apply a variant to a transcript and check resulting CDS sequence, protein sequence and exon coordinates
void	TestCasesBase.checkApplyDel(Variant variant, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)
void	TestCasesBase.checkApplyIns(Variant variant, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)
void	TestCasesBase.checkApplyMixed(Variant variant, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)
void	TestCasesBase.checkApplyMnp(Variant variant, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)
void	TestCasesBase.checkApplySnp(Variant variant, java.lang.String expectedCds, java.lang.String expectedProtein, int exonRank, int expectedExon1Start, int expectedExon1End)
protected void	TestCasesBase.checkEffect(Variant variant, EffectType effectExpected)
protected void	TestCasesBase.checkEffect(Variant variant, EffectType effectExpected, EffectType effectNotExpected, VariantEffect.EffectImpact impact)
void	TestGenome.checkEffect(Variant variant, EffectType effectTypeExpected, VariantEffect.EffectImpact effectImpactExpected, int countMatchExpected)	Apply a predictor to a variant and check whether the expected number of matches are found
protected void	TestCasesStructuralDel.checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void	TestCasesStructuralDup.checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void	TestCasesStructuralInv.checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns)
protected void	TestCasesStructuralInv.checkEffects(Variant variant, EffectType[] expEffs, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact, java.lang.String[] expAnns, Gene[] genesToAdd)
protected void	TestCasesStructuralTranslocations.checkEffects(Variant variant, EffectType[] expEffs, EffectType[] notExpEffs, java.lang.String[] expHgvsp, java.lang.String[] expHgvsc, VariantEffect.EffectImpact expectedImpact)

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 java.util.LinkedList<Variant>	VcfEntry.variants

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

Modifier and Type	Method	Description
java.util.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
java.lang.String	VcfEntry.getInfo(java.lang.String key, Variant var)	Get an INFO field matching a variant

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

Constructor	Description
VariantVcfEntry(Variant variant, VcfEntry vcfEntry)