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An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *- Author: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