Package htsjdk.samtools

Interface CRAMIndexer

All Known Implementing Classes:
CRAMBAIIndexer, CRAMCRAIIndexer
public interface CRAMIndexer
Interface for indexing CRAM.

  • Method Summary

    Modifier and Type
    Method
    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 Details

    • 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.