Class LinearIndex


  • public class LinearIndex
    extends Object
    The linear index associated with a given reference in a BAM index.
    • Field Detail

      • MAX_LINEAR_INDEX_SIZE

        public static final int MAX_LINEAR_INDEX_SIZE
    • Constructor Detail

      • LinearIndex

        public LinearIndex​(int referenceSequence,
                           int indexStart,
                           long[] indexEntries)
    • Method Detail

      • getReferenceSequence

        public int getReferenceSequence()
      • size

        public int size()
      • get

        public long get​(int index)
      • convertToLinearIndexOffset

        public static int convertToLinearIndexOffset​(int contigPos)
      • getMinimumOffset

        public long getMinimumOffset​(int startPos)
        Gets the minimum offset of any alignment start appearing in this index, according to the linear index.
        Parameters:
        startPos - Starting position for this query.
        Returns:
        The minimum offset, in chunk format, of any read appearing in this position.
      • getIndexEntries

        public long[] getIndexEntries()
        Direct access to the array. Be careful!
        Returns:
        The elements of the linear index.
      • getIndexStart

        public int getIndexStart()
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object