org.broadinstitute.hellbender.utils.read.markduplicates

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 Summary

Modifier and Type	Method and Description
void	put(int mateSequenceIndex, java.lang.String key, ReadEndsForMarkDuplicates readEnds) Store the element in the map with the given key.
ReadEndsForMarkDuplicates	remove(int mateSequenceIndex, java.lang.String key) Remove element with given key from the map.
int	size()
int	sizeInRam()

Method Detail

remove

ReadEndsForMarkDuplicates remove(int mateSequenceIndex,
                                 java.lang.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,
         java.lang.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()