Uses of Class
org.snpeff.interval.Variant
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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)
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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()
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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 + InDelVariant
VariantNonRef. getVariantRef()
Variant
Variant. realignLeft()
Create a new variant realigning it towards the leftmost positionVariant
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 variantTranscript
Transcript. apply(Variant variant)
Create a new transcript after applying changes in variantprotected 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 transcriptint
Upstream. distanceToTr(Variant variant)
Distance to transcriptErrorWarningType
Exon. sanityCheck(Variant variant)
Check that the base in the exon corresponds with the one in the SNPErrorWarningType
Transcript. 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 Constructor Description VariantNonRef(Variant variant, Variant variantRef)
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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 variantConstructors 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)
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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 effectvoid
VariantEffects. add(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, java.lang.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)
java.lang.String
EffectType. toSequenceOntology(EffFormatVersion formatVersion, Variant variant)
VariantEffects
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'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)
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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 listMethod 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 coordinatesvoid
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 foundprotected 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)
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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 VcfEntryMethods 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 variantConstructors in org.snpeff.vcf with parameters of type Variant Constructor Description VariantVcfEntry(Variant variant, VcfEntry vcfEntry)
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