Interface ReadEndsForMarkDuplicatesMap

  • All Known Implementing Classes:
    DiskBasedReadEndsForMarkDuplicatesMap

    public interface ReadEndsForMarkDuplicatesMap
    Interface for storing and retrieving ReadEnds objects. An implementation may be disk-based to reduce memory footprint.
    • Method Detail

      • remove

        ReadEndsForMarkDuplicates remove​(int mateSequenceIndex,
                                         String key)
        Remove element with given key from the map. Because an implementation may be disk-based, the object returned may not be the same object that was put into the map
        Parameters:
        mateSequenceIndex - must agree with the value used when the object was put into the map
        key - typically, concatenation of read group ID and read name
        Returns:
        null if the key is not found, otherwise the object removed.
      • put

        void put​(int mateSequenceIndex,
                 String key,
                 ReadEndsForMarkDuplicates readEnds)
        Store the element in the map with the given key. It is assumed that the element is not already present in the map.
        Parameters:
        mateSequenceIndex - use to optimize storage & retrieval. The same value must be used when trying to remove this element. It is not valid to store the same key with two different mateSequenceIndexes.
        key - typically, concatenation of read group ID and read name
        readEnds - the object to be stored
      • size

        int size()
        Returns:
        number of elements stored in map
      • sizeInRam

        int sizeInRam()
        Returns:
        number of elements stored in RAM. Always <= size()