Class ReadEnds

    • Field Detail

      • libraryId

        public short libraryId
      • orientation

        public byte orientation
      • read1ReferenceIndex

        public int read1ReferenceIndex
      • read1Coordinate

        public int read1Coordinate
      • read2ReferenceIndex

        public int read2ReferenceIndex
      • read2Coordinate

        public int read2Coordinate
      • readGroup

        public short readGroup
      • orientationForOpticalDuplicates

        public byte orientationForOpticalDuplicates
        For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate
      • isOpticalDuplicate

        public transient boolean isOpticalDuplicate
        A *transient* flag marking this read end as being an optical duplicate.
    • Constructor Detail

      • ReadEnds

        public ReadEnds()