Package htsjdk.samtools.util

Class WholeGenomeReferenceSequenceMask

java.lang.Object
htsjdk.samtools.util.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 Details

    • WholeGenomeReferenceSequenceMask

      public WholeGenomeReferenceSequenceMask(SAMFileHeader header)

  • Method Details

    • 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

    • getMaxSequenceIndex

      public int getMaxSequenceIndex()
      Specified by:
      getMaxSequenceIndex in interface ReferenceSequenceMask
      Returns:
      Largest sequence index for which there are set bits.

    • getMaxPosition

      public int getMaxPosition()
      Specified by:
      getMaxPosition in interface ReferenceSequenceMask
      Returns:
      the largest position on the last sequence index