Constructor Detail

• CRAMCRAIIndexer

  public CRAMCRAIIndexer​(OutputStream os,
                         SAMFileHeader samHeader)

  Create a CRAMCRAIIndexer that writes to the given output stream.

  Parameters:

  os - output stream to which the index will be written

  samHeader - SAMFileHeader - user to verify sort order

Method Detail

• processContainer

  public void processContainer​(Container container)

  Create index entries for a single container.

  Parameters:

  container - the container to index

• addEntry

  public void addEntry​(CRAIEntry entry)

• finish

  public void finish()

  Finish creating the index by writing the accumulated entries out to the stream.

• writeIndex

  public static void writeIndex​(SeekableStream cramStream,
                                OutputStream craiStream)

  Generate and write a CRAI index to an output stream from a CRAM input stream

  Parameters:

  cramStream - CRAM stream to index; must be coordinate sorted

  craiStream - stream for output index

• readIndex

  public static CRAIIndex readIndex​(InputStream is)

  Read an input stream containing a .crai index and return a CRAIIndex object.

  Parameters:

  is - Input stream to read

  Returns:

  A CRAIIndex object representing the index.