Class SAMCodecV1_0

Method Details

• getVersion

  public HtsVersion getVersion()

  Description copied from interface: HtsCodec

  Get the version of the file format returned by HtsCodec.getFileFormat() that is supported by this codec.

  Returns:

  the file format version (HtsVersion) supported by this codec

• getDecoder

  public SAMDecoder getDecoder(Bundle inputBundle, ReadsDecoderOptions decoderOptions)

  Description copied from interface: HtsCodec

  Get an HtsDecoder to decode the provided inputs. The input bundle must contain resources of the type required by this codec. To find a codec appropriate for decoding a given resource, use an HtsCodecResolver obtained from an HtsCodecRegistry.

  The framework will never call thi* method unless either HtsCodec.ownsURI(IOPath), or HtsCodec.canDecodeURI(IOPath) and HtsCodec.canDecodeSignature(SignatureStream, String) (IOPath)} return true for inputBundle.

  Parameters:

  inputBundle - input to be decoded. To get a decoder for use with index queries that use HtsQuery methods, the bundle must contain an index resource.

  decoderOptions - options for the decoder to use

  Returns:

  an HtsDecoder that can decode the provided inputs

• getEncoder

  public SAMEncoder getEncoder(Bundle outputBundle, ReadsEncoderOptions encoderOptions)

  Description copied from interface: HtsCodec

  Get an HtsEncoder to encode to the provided outputs. The output bundle must contain resources of the type required by this codec. To find a codec appropriate for encoding a given resource, use an HtsCodecResolver obtained from an HtsCodecRegistry.

  The framework will never call this method unless either HtsCodec.ownsURI(IOPath), or HtsCodec.canDecodeURI(IOPath) returned true for outputBundle.

  Parameters:

  outputBundle - target output for the encoder

  encoderOptions - encoder options to use

  Returns:

  an HtsEncoder suitable for writing to the provided outputs

• runVersionUpgrade

  public boolean runVersionUpgrade(HtsVersion sourceCodecVersion, HtsVersion targetCodecVersion)