Class WholeGenomeReferenceSequenceMask

  • All Implemented Interfaces:
    ReferenceSequenceMask

    public class WholeGenomeReferenceSequenceMask
    extends Object
    implements ReferenceSequenceMask
    Implementation of ReferenceSequenceMask that indicates that all the loci in the sequence dictionary are of interest.
    • Constructor Detail

      • WholeGenomeReferenceSequenceMask

        public WholeGenomeReferenceSequenceMask​(SAMFileHeader header)
    • Method Detail

      • get

        public boolean get​(int sequenceIndex,
                           int position)
        Description copied from interface: ReferenceSequenceMask
        It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
        Specified by:
        get in interface ReferenceSequenceMask
        Returns:
        true if the mask is set for the given sequence and position
      • nextPosition

        public int nextPosition​(int sequenceIndex,
                                int position)
        Description copied from interface: ReferenceSequenceMask
        It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
        Specified by:
        nextPosition in interface ReferenceSequenceMask
        Returns:
        the next pos on the given sequence >= position that is set, or -1 if there are no more set positions