Package picard.sam.markduplicates.util

Class MemoryBasedReadEndsForMarkDuplicatesMap

java.lang.Object
picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
All Implemented Interfaces:
ReadEndsForMarkDuplicatesMap
public class MemoryBasedReadEndsForMarkDuplicatesMap extends Object implements ReadEndsForMarkDuplicatesMap
Map from String to ReadEnds object. Memory-based implementation. Used for MarkDuplicates.

  • Constructor Details

    • MemoryBasedReadEndsForMarkDuplicatesMap

      public MemoryBasedReadEndsForMarkDuplicatesMap()

  • Method Details

    • remove

      public ReadEndsForMarkDuplicates remove(int mateSequenceIndex, String key)
      Description copied from interface: ReadEndsForMarkDuplicatesMap
      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
      Specified by:
      remove in interface ReadEndsForMarkDuplicatesMap
      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

      public void put(int mateSequenceIndex, String key, ReadEndsForMarkDuplicates readEnds)
      Description copied from interface: ReadEndsForMarkDuplicatesMap
      Store the element in the map with the given key. It is assumed that the element is not already present in the map.
      Specified by:
      put in interface ReadEndsForMarkDuplicatesMap
      Parameters:
      mateSequenceIndex - use to optimize storage invalid input: '&' 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

      public int size()
      Specified by:
      size in interface ReadEndsForMarkDuplicatesMap
      Returns:
      number of elements stored in map

    • sizeInRam

      public int sizeInRam()
      Specified by:
      sizeInRam in interface ReadEndsForMarkDuplicatesMap
      Returns:
      number of elements stored in RAM. Always invalid input: '<'= size()