htsjdk.samtools

Interface CRAMIndexer

All Known Implementing Classes:

CRAMBAIIndexer, CRAMCRAIIndexer

public interface CRAMIndexer

Interface for indexing CRAM.

Method Summary

Modifier and Type	Method and Description
void	finish() Finish creating the index by writing the accumulated entries out.
void	processContainer(Container container, ValidationStringency validationStringency) Create index entries for a single container.

Method Detail

processContainer

void processContainer(Container container,
                      ValidationStringency validationStringency)

Create index entries for a single container.

Parameters:

container - the container to index

validationStringency - stringency for validating records (used when processing multi-reference slices, since creating an index on a multi-ref slices requires actually decoding the records in order to resove the constituent reference spans}

finish

void finish()

Finish creating the index by writing the accumulated entries out.