Package htsjdk.samtools.cram.encoding.external

Class ExternalByteArrayEncoding

java.lang.Object
htsjdk.samtools.cram.encoding.CRAMEncoding<T>
htsjdk.samtools.cram.encoding.external.ExternalEncoding<byte[]>
htsjdk.samtools.cram.encoding.external.ExternalByteArrayEncoding
public final class ExternalByteArrayEncoding extends ExternalEncoding<byte[]>

  • Constructor Details

    • ExternalByteArrayEncoding

      public ExternalByteArrayEncoding(int externalBlockContentId)

  • Method Details

    • fromSerializedEncodingParams

      public static ExternalByteArrayEncoding fromSerializedEncodingParams(byte[] serializedParams)
      Create a new instance of this encoding using the (ITF8 encoded) serializedParams.
      Parameters:
      serializedParams -
      Returns:
      ExternalByteArrayEncoding with parameters populated from serializedParams

    • toSerializedEncodingParams

      public byte[] toSerializedEncodingParams()
      Description copied from class: CRAMEncoding
      Serialize encoding parameters to an ITF8-encoded byte array. By convention, each subclass should have a corresponding and symmetric "fromSerializedEncodingParams" that returns a new instance of that encoding populated with values from the serialized encoding params.
      Overrides:
      toSerializedEncodingParams in class ExternalEncoding<byte[]>
      Returns:
      a byte array containing the encoding's parameter values encoded as an ITF8 stream.

    • buildCodec

      public CRAMCodec<byte[]> buildCodec(SliceBlocksReadStreams sliceBlocksReadStreams, SliceBlocksWriteStreams sliceBlocksWriteStreams)
      Description copied from class: CRAMEncoding
      Instantiate the codec represented by this encoding by supplying it with the appropriate streams
      Specified by:
      buildCodec in class CRAMEncoding<byte[]>
      Parameters:
      sliceBlocksReadStreams - the core block bit stream a CoreCodec will read from
      sliceBlocksWriteStreams - the core block bit stream a CoreCodec will write to
      Returns:
      a newly instantiated codec

    • toString

      public String toString()
      Overrides:
      toString in class ExternalEncoding<byte[]>