Class ReadsEncoderOptions

Method Details

• isPreSorted

  public boolean isPreSorted()

  Get the preSorted setting for these options. Default value is false. If isPresorted is false, output will be sorted as needed on write.

  Returns:

  true if preSorted is true, otherwise false

• setPreSorted

  public ReadsEncoderOptions setPreSorted(boolean preSorted)

  Set the preSorted setting for these options. Default value is false. If preSorted is false, output will be sorted as needed on write.

  Parameters:

  preSorted - the preSorted state for these options

  Returns:

  updated ReadsEncoderOptions

• getBAMEncoderOptions

  public BAMEncoderOptions getBAMEncoderOptions()

  Get the BAMEncoderOptions for these ReadsEncoderOptions. Defaults to default BAMEncoderOptions.

  Returns:

  the BAMEncoderOptions for these ReadsEncoderOptions

• setBAMEncoderOptions

  public ReadsEncoderOptions setBAMEncoderOptions(BAMEncoderOptions bamEncoderOptions)

  Set the BAMEncoderOptions for these ReadsEncoderOptions. Defaults values are default BAMEncoderOptions.

  Parameters:

  bamEncoderOptions - BAMEncoderOptions to use for these ReadsEncoderOptions

  Returns:

  updated ReadsEncoderOptions

• getCRAMEncoderOptions

  public CRAMEncoderOptions getCRAMEncoderOptions()

  Get the CRAMEncoderOptions for this ReadsEncoderOptions. Default values are default CRAMEncoderOptions.

  Returns:

  the CRAMEncoderOptions for this ReadsEncoderOptions

• setCRAMEncoderOptions

  public ReadsEncoderOptions setCRAMEncoderOptions(CRAMEncoderOptions cramEncoderOptions)

  Set the CRAMEncoderOptions for these ReadsEncoderOptions. Defaults to default CRAMEncoderOptions.

  Parameters:

  cramEncoderOptions - the CRAMEncoderOptions for these ReadsEncoderOptions

  Returns:

  updated ReadsEncoderOptions