Field Detail

• readNamesIncluded

  public boolean readNamesIncluded

• APDelta

  public boolean APDelta

• encodingMap

  public Map<DataSeries,​EncodingParams> encodingMap

• tMap

  public Map<Integer,​EncodingParams> tMap

• externalCompressors

  public final Map<Integer,​ExternalCompressor> externalCompressors

• substitutionMatrix

  public SubstitutionMatrix substitutionMatrix

• externalIds

  public List<Integer> externalIds

• dictionary

  public byte[][][] dictionary

Constructor Detail

• CompressionHeader

  public CompressionHeader()

Method Detail

• getTagIds

  public byte[][] getTagIds​(int id)

• write

  public void write​(Version cramVersion,
                    OutputStream blockStream)

  Write this CompressionHeader out to an internal OutputStream, wrap it in a Block, and write that Block out to the passed-in OutputStream.

  Parameters:

  cramVersion - the CRAM major version number

  blockStream - the stream to write to

• read

  public static CompressionHeader read​(int cramVersion,
                                       InputStream blockStream)

  Read a COMPRESSION_HEADER Block from an InputStream and return its contents as a CompressionHeader We do this instead of reading the InputStream directly because the Block content may be compressed

  Parameters:

  cramVersion - the CRAM version

  blockStream - the stream to read from

  Returns:

  a new CompressionHeader from the input