Constructor Detail

• ContainerIO

  public ContainerIO()

Method Detail

• readContainer

  public static Container readContainer(Version version,
                                        InputStream inputStream)
                                 throws IOException

  Reads a CRAM container from the input stream. Returns an EOF container when there is no more data or the EOF marker found.

  Parameters:

  version - CRAM version to expect

  inputStream - the stream to read from

  Returns:

  a new container object read from the stream

  Throws:

  IOException - as per java IO contract

• readContainerHeader

  public static Container readContainerHeader(int major,
                                              InputStream inputStream)
                                       throws IOException

  Reads container header only from a InputStream.

  Parameters:

  major - the CRAM version to assume

  inputStream - the input stream to read from

  Returns:

  a new Container object with container header values filled out but empty body (no slices and blocks).

  Throws:

  IOException - as per java IO contract

• writeContainerHeader

  public static int writeContainerHeader(int major,
                                         Container container,
                                         OutputStream outputStream)
                                  throws IOException

  Writes a Container header information to a OutputStream.

  Parameters:

  major - the CRAM version to assume

  container - the container holding the header to write

  outputStream - the stream to write to

  Returns:

  the number of bytes written

  Throws:

  IOException - as per java IO contract

• writeContainer

  public static int writeContainer(Version version,
                                   Container container,
                                   OutputStream outputStream)
                            throws IOException

  Writes a complete Container with it's header to a OutputStream. The method is aware of file header containers and is suitable for general purpose use: basically any container is allowed.

  Parameters:

  version - the CRAM version to assume

  container - the container to write

  outputStream - the stream to write to

  Returns:

  the number of bytes written out

  Throws:

  IOException - as per java IO contract

• getByteSize

  public static long getByteSize(Version version,
                                 Container container)

  Calculates the byte size of a container based on the CRAM version.

  Parameters:

  version - the CRAM version to assume

  container - the container to be weighted

  Returns:

  the total number of bytes the container would occupy if written out