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An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *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