Package org.snpeff.vcf

Class VcfEffect

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    An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *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

    • Field Detail

      • debug

        public static boolean debug

      • ANN_FIELD_NAMES

        public static java.lang.String[] ANN_FIELD_NAMES

      • EFF_FIELD_NAMES

        public static java.lang.String[] EFF_FIELD_NAMES

    • Constructor Detail

      • VcfEffect

        public VcfEffect​(java.lang.String effectString)
        Constructor: Guess format version

      • VcfEffect

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

      • VcfEffect

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

    • Method Detail

      • infoFieldName

        public static java.lang.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​(java.lang.String effectString)
        Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-version

      • getAa

        public java.lang.String getAa()

      • setAa

        public void setAa​(java.lang.String aa)

      • getAaLen

        public int getAaLen()

      • setAaLen

        public void setAaLen​(int aaLen)

      • getAaPos

        public int getAaPos()

      • getAllele

        public java.lang.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()

      • getCodon

        public java.lang.String getCodon()

      • setCodon

        public void setCodon​(java.lang.String codon)

      • getDistance

        public int getDistance()

      • getEffectDetails

        public java.lang.String getEffectDetails()

      • setEffectDetails

        public void setEffectDetails​(java.lang.String effectDetails)

      • getEffectsStr

        public java.lang.String getEffectsStr()

      • getEffectsStrSo

        public java.lang.String getEffectsStrSo()

      • getEffectType

        public EffectType getEffectType()

      • setEffectType

        public void setEffectType​(EffectType effect)

      • getEffectTypes

        public java.util.List<EffectType> getEffectTypes()

      • getEffectTypesStr

        public java.lang.String getEffectTypesStr()

      • getEffString

        public java.lang.String getEffString()

      • getErrorsWarning

        public java.lang.String getErrorsWarning()

      • getExonId

        public java.lang.String getExonId()

      • setExonId

        public void setExonId​(java.lang.String exonId)

      • getFeatureId

        public java.lang.String getFeatureId()

      • getFeatureType

        public java.lang.String getFeatureType()

      • getFieldByName

        public java.lang.String getFieldByName​(java.lang.String fieldName)
        Get a subfield by name

      • setFormatVersion

        public void setFormatVersion​(EffFormatVersion formatVersion)

      • getGeneId

        public java.lang.String getGeneId()

      • setGeneId

        public void setGeneId​(java.lang.String geneId)

      • getGeneName

        public java.lang.String getGeneName()

      • setGeneName

        public void setGeneName​(java.lang.String geneName)

      • getGenotype

        public java.lang.String getGenotype()

      • setGenotype

        public void setGenotype​(java.lang.String genotype)

      • getHgvsC

        public java.lang.String getHgvsC()

      • getHgvsDna

        public java.lang.String getHgvsDna()

      • getHgvsP

        public java.lang.String getHgvsP()

      • getHgvsProt

        public java.lang.String getHgvsProt()

      • getRank

        public int getRank()

      • getRankMax

        public int getRankMax()

      • getTranscriptId

        public java.lang.String getTranscriptId()

      • setTranscriptId

        public void setTranscriptId​(java.lang.String transcriptId)

      • getVcfFieldString

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

      • getVcfFieldString

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

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object