Enum EffFormatVersion

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Comparable<EffFormatVersion>

    public enum EffFormatVersion
    extends java.lang.Enum<EffFormatVersion>
    VcfFields in SnpEff version 2.X have a different format than 3.X As of version 4.1 we switch to a standard annotation format
    • Field Detail

      • DEFAULT_FORMAT_VERSION

        public static final EffFormatVersion DEFAULT_FORMAT_VERSION
      • VCF_INFO_EFF_NAME

        public static final java.lang.String VCF_INFO_EFF_NAME
        See Also:
        Constant Field Values
      • VCF_INFO_ANN_NAME

        public static final java.lang.String VCF_INFO_ANN_NAME
        See Also:
        Constant Field Values
      • VCF_INFO_ANN_NAMES

        public static final java.lang.String[] VCF_INFO_ANN_NAMES
      • EFFECT_TYPE_SEPARATOR

        public static final java.lang.String EFFECT_TYPE_SEPARATOR
        See Also:
        Constant Field Values
      • EFFECT_TYPE_SEPARATOR_OLD

        public static final java.lang.String EFFECT_TYPE_SEPARATOR_OLD
        See Also:
        Constant Field Values
      • vcfInfoNames

        protected static java.util.Set<java.lang.String> vcfInfoNames
    • Method Detail

      • values

        public static EffFormatVersion[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
        for (EffFormatVersion c : EffFormatVersion.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static EffFormatVersion valueOf​(java.lang.String name)
        Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
        Parameters:
        name - the name of the enum constant to be returned.
        Returns:
        the enum constant with the specified name
        Throws:
        java.lang.IllegalArgumentException - if this enum type has no constant with the specified name
        java.lang.NullPointerException - if the argument is null
      • isEffectVcfInfoField

        public static boolean isEffectVcfInfoField​(java.lang.String key)
        Is this one of the VCF INFO keys?
      • infoFieldName

        public java.lang.String infoFieldName()
        Get INF field name for corresponding format
      • isAnn

        public boolean isAnn()
        Is this an 'ANN' format?
      • isEff

        public boolean isEff()
        Id this an 'EFF' format?
      • isFullVersion

        public boolean isFullVersion()
        Is this format fully specified? I.e. does it have version number?
      • separator

        public java.lang.String separator()
        Multiple effect separator
      • separatorSplit

        public java.lang.String separatorSplit()
        Multiple effect separator: Split regex
      • vcfHeader

        public java.lang.String vcfHeader()
        VCF header for each format type