Interface ReferenceSequenceMask

All Known Implementing Classes:
IntervalListReferenceSequenceMask, WholeGenomeReferenceSequenceMask

public interface ReferenceSequenceMask
Interface for specifying loci of interest for genotype calling and other operations. It is a requirement that the sequences be probed in ascending order.
  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    get(int sequenceIndex, int position)
    It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
    int
     
    int
     
    int
    nextPosition(int sequenceIndex, int position)
    It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
  • Method Details

    • get

      boolean get(int sequenceIndex, int position)
      It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
      Returns:
      true if the mask is set for the given sequence and position
    • nextPosition

      int nextPosition(int sequenceIndex, int position)
      It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
      Returns:
      the next pos on the given sequence >= position that is set, or -1 if there are no more set positions
    • getMaxSequenceIndex

      int getMaxSequenceIndex()
      Returns:
      Largest sequence index for which there are set bits.
    • getMaxPosition

      int getMaxPosition()
      Returns:
      the largest position on the last sequence index