Class CRAMDecoderOptions

Method Details

• getReferenceSource

  public Optional<CRAMReferenceSource> getReferenceSource()

  Get the CRAMReferenceSource for these options.

  Returns:

  the CRAMReferenceSource for these options, or Optional.empty() if none

• setReferenceSource

  public CRAMDecoderOptions setReferenceSource(CRAMReferenceSource referenceSource)

  Set the CRAMReferenceSource for these options. Mutually exclusive with setReferencePath(IOPath), which must be set to null in order to set a CRAMReferenceSource.

  Parameters:

  referenceSource - the CRAMReferenceSource for these options. May be null.

  Returns:

  updated CRAMDecoderOptions

  Throws:

  IllegalArgumentException - if a reference path is already set on these options

• getReferencePath

  public Optional<IOPath> getReferencePath()

  Get the reference path for these options.

  Returns:

  the reference path for these options, or Optional.empty() if none.

• setReferencePath

  public CRAMDecoderOptions setReferencePath(IOPath referencePath)

  Set the reference path for these options. Mutually exclusive with setReferenceSource(CRAMReferenceSource), which must be set to null in order to set a reference path.

  Parameters:

  referencePath - The path to use. may be null.

  Returns:

  updated CRAMDecoderOptions

  Throws:

  IllegalArgumentException - if a reference source is already set on these options