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()