Package org.snpeff.vcf
Class VcfEffect
java.lang.Object
org.snpeff.vcf.VcfEffect
An 'ANN' or 'EFF' entry in a VCF INFO field
Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12)
*
- Author:
- pablocingolani
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionConstructor: Guess format versionVcfEffect
(String effectString, EffFormatVersion formatVersion) Constructor: Force format versionVcfEffect
(VariantEffect variantEffect, EffFormatVersion formatVersion) VcfEffect
(VariantEffect variantEffect, EffFormatVersion formatVersion, boolean useSequenceOntology, boolean useFirstEffect) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addEffectType
(EffectType effectType) Guess effect format versionprotected EffFormatVersion
formatVersion
(String effectString) Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-versiongetAa()
int
getAaLen()
int
getAaPos()
int
int
int
int
getCodon()
int
getFieldByName
(String fieldName) Get a subfield by namegetHgvsC()
getHgvsP()
int
getRank()
int
String from VCF file (original, unparsed, string)getVcfFieldString
(int index) Get a subfield as an indexboolean
hasEffectType
(EffectType effType) Does it have 'effType' ?static String
infoFieldName
(EffFormatVersion formatVersion) Get info field name based on format versionvoid
void
setAaLen
(int aaLen) void
setBioType
(BioType bioType) void
setCoding
(VariantEffect.Coding coding) void
void
setEffectDetails
(String effectDetails) void
setEffectType
(EffectType effect) void
void
setFormatVersion
(EffFormatVersion formatVersion) void
setFunClass
(VariantEffect.FunctionalClass funClass) void
void
setGeneName
(String geneName) void
setGenotype
(String genotype) void
setImpact
(VariantEffect.EffectImpact impact) void
setTranscriptId
(String transcriptId) void
setUseFirstEffect
(boolean useFirstEffect) void
setUseGeneId
(boolean useGeneId) void
setUseHgvs
(boolean useHgvs) String[]
Split a 'effect' string to an array of stringstoString()
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Field Details
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debug
public static boolean debug -
ANN_FIELD_NAMES
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EFF_FIELD_NAMES
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Constructor Details
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VcfEffect
Constructor: Guess format version -
VcfEffect
Constructor: Force format version- Parameters:
formatVersion
- : If null, will try to guess it
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VcfEffect
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VcfEffect
public VcfEffect(VariantEffect variantEffect, EffFormatVersion formatVersion, boolean useSequenceOntology, boolean useFirstEffect)
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Method Details
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infoFieldName
Get info field name based on format version -
addEffectType
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formatVersion
Guess effect format version -
formatVersion
Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-version -
getAa
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setAa
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getAaLen
public int getAaLen() -
setAaLen
public void setAaLen(int aaLen) -
getAaPos
public int getAaPos() -
getAllele
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getBioType
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setBioType
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getcDnaLen
public int getcDnaLen() -
getcDnaPos
public int getcDnaPos() -
getCdsLen
public int getCdsLen() -
getCdsPos
public int getCdsPos() -
getCoding
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setCoding
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getCodon
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setCodon
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getDistance
public int getDistance() -
getEffectDetails
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setEffectDetails
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getEffectsStr
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getEffectsStrSo
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getEffectType
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setEffectType
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getEffectTypes
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getEffectTypesStr
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getEffString
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getErrorsWarning
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getExonId
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setExonId
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getFeatureId
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getFeatureType
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getFieldByName
Get a subfield by name -
getFormatVersion
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setFormatVersion
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getFunClass
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setFunClass
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getGeneId
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setGeneId
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getGeneName
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setGeneName
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getGenotype
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setGenotype
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getHgvsC
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getHgvsDna
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getHgvsP
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getHgvsProt
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getImpact
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setImpact
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getRank
public int getRank() -
getRankMax
public int getRankMax() -
getTranscriptId
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setTranscriptId
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getVcfFieldString
String from VCF file (original, unparsed, string) -
getVcfFieldString
Get a subfield as an index -
hasEffectType
Does it have 'effType' ? -
setUseFirstEffect
public void setUseFirstEffect(boolean useFirstEffect) -
setUseGeneId
public void setUseGeneId(boolean useGeneId) -
setUseHgvs
public void setUseHgvs(boolean useHgvs) -
split
Split a 'effect' string to an array of strings -
toString
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