Package org.snpeff.vcf

Class VcfEffect

java.lang.Object
org.snpeff.vcf.VcfEffect
public class VcfEffect extends 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An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *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

  • Field Details

    • debug

      public static boolean debug

    • ANN_FIELD_NAMES

      public static String[] ANN_FIELD_NAMES

    • EFF_FIELD_NAMES

      public static String[] EFF_FIELD_NAMES

  • Constructor Details

    • VcfEffect

      public VcfEffect(String effectString)
      Constructor: Guess format version

    • VcfEffect

      public VcfEffect(String effectString, EffFormatVersion formatVersion)
      Constructor: Force format version
      Parameters:
      formatVersion - : If null, will try to guess it

    • VcfEffect

      public VcfEffect(VariantEffect variantEffect, EffFormatVersion formatVersion)

    • VcfEffect

      public VcfEffect(VariantEffect variantEffect, EffFormatVersion formatVersion, boolean useSequenceOntology, boolean useFirstEffect)

  • Method Details

    • infoFieldName

      public static String infoFieldName(EffFormatVersion formatVersion)
      Get info field name based on format version

    • addEffectType

      public void addEffectType(EffectType effectType)

    • formatVersion

      public EffFormatVersion formatVersion()
      Guess effect format version

    • formatVersion

      protected EffFormatVersion formatVersion(String effectString)
      Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-version

    • getAa

      public String getAa()

    • setAa

      public void setAa(String aa)

    • getAaLen

      public int getAaLen()

    • setAaLen

      public void setAaLen(int aaLen)

    • getAaPos

      public int getAaPos()

    • getAllele

      public String getAllele()

    • getBioType

      public BioType getBioType()

    • setBioType

      public void setBioType(BioType bioType)

    • getcDnaLen

      public int getcDnaLen()

    • getcDnaPos

      public int getcDnaPos()

    • getCdsLen

      public int getCdsLen()

    • getCdsPos

      public int getCdsPos()

    • getCoding

      public VariantEffect.Coding getCoding()

    • setCoding

      public void setCoding(VariantEffect.Coding coding)

    • getCodon

      public String getCodon()

    • setCodon

      public void setCodon(String codon)

    • getDistance

      public int getDistance()

    • getEffectDetails

      public String getEffectDetails()

    • setEffectDetails

      public void setEffectDetails(String effectDetails)

    • getEffectsStr

      public String getEffectsStr()

    • getEffectsStrSo

      public String getEffectsStrSo()

    • getEffectType

      public EffectType getEffectType()

    • setEffectType

      public void setEffectType(EffectType effect)

    • getEffectTypes

      public List<EffectType> getEffectTypes()

    • getEffectTypesStr

      public String getEffectTypesStr()

    • getEffString

      public String getEffString()

    • getErrorsWarning

      public String getErrorsWarning()

    • getExonId

      public String getExonId()

    • setExonId

      public void setExonId(String exonId)

    • getFeatureId

      public String getFeatureId()

    • getFeatureType

      public String getFeatureType()

    • getFieldByName

      public String getFieldByName(String fieldName)
      Get a subfield by name

    • getFormatVersion

      public EffFormatVersion getFormatVersion()

    • setFormatVersion

      public void setFormatVersion(EffFormatVersion formatVersion)

    • getFunClass

      public VariantEffect.FunctionalClass getFunClass()

    • setFunClass

      public void setFunClass(VariantEffect.FunctionalClass funClass)

    • getGeneId

      public String getGeneId()

    • setGeneId

      public void setGeneId(String geneId)

    • getGeneName

      public String getGeneName()

    • setGeneName

      public void setGeneName(String geneName)

    • getGenotype

      public String getGenotype()

    • setGenotype

      public void setGenotype(String genotype)

    • getHgvsC

      public String getHgvsC()

    • getHgvsDna

      public String getHgvsDna()

    • getHgvsP

      public String getHgvsP()

    • getHgvsProt

      public String getHgvsProt()

    • getImpact

      public VariantEffect.EffectImpact getImpact()

    • setImpact

      public void setImpact(VariantEffect.EffectImpact impact)

    • getRank

      public int getRank()

    • getRankMax

      public int getRankMax()

    • getTranscriptId

      public String getTranscriptId()

    • setTranscriptId

      public void setTranscriptId(String transcriptId)

    • getVcfFieldString

      public String getVcfFieldString()
      String from VCF file (original, unparsed, string)

    • getVcfFieldString

      public String getVcfFieldString(int index)
      Get a subfield as an index

    • hasEffectType

      public boolean hasEffectType(EffectType effType)
      Does it have 'effType' ?

    • setUseFirstEffect

      public void setUseFirstEffect(boolean useFirstEffect)

    • setUseGeneId

      public void setUseGeneId(boolean useGeneId)

    • setUseHgvs

      public void setUseHgvs(boolean useHgvs)

    • split

      public String[] split(String eff)
      Split a 'effect' string to an array of strings

    • toString

      public String toString()
      Overrides:
      toString in class Object