Class TabixFormat

  • All Implemented Interfaces:
    Cloneable

    public class TabixFormat
    extends Object
    implements Cloneable
    The values in a Tabix header that define the format of the file being indexed, e.g. gff, bed, vcf
    • Field Detail

      • GFF

        public static TabixFormat GFF
        Predefined headers for known formats
      • flags

        public int flags
        Describes interpretation of file being indexed. See FLAGS constants above.
      • sequenceColumn

        public int sequenceColumn
        One-based index of the column in the file being indexed containing the sequence name
      • startPositionColumn

        public int startPositionColumn
        One-based index of the column in the file being indexed containing the start position.
      • endPositionColumn

        public int endPositionColumn
        One-based index of the column in the file being indexed containing the end position. Zero implies there is no end position column.
      • metaCharacter

        public char metaCharacter
        Lines in the file being indexed that start with this character are ignored.
      • numHeaderLinesToSkip

        public int numHeaderLinesToSkip
        TODO: This is written, and part of the index header, but does not appear to be used.
    • Constructor Detail

      • TabixFormat

        public TabixFormat()
      • TabixFormat

        public TabixFormat​(int flags,
                           int sequenceColumn,
                           int startPositionColumn,
                           int endPositionColumn,
                           char metaCharacter,
                           int numHeaderLinesToSkip)