gunz_cm.compressions.zstd_decoder#

Module contents#

Zstd decoder wrapper for GZCM v3 compression.

Uses zlib as fallback since zstandard may not be installed.

Examples

class gunz_cm.compressions.zstd_decoder.ZstdDecoder(tile_size: int = 256, resolution: int = 50000, dtype: ~numpy.dtype = <class 'numpy.uint32'>, use_zstd: bool = True)[source]#

Bases: object

Zstd decoder for contact matrix tiles.

Parameters:

  • tile_size (int, default=256) – Tile size for block processing.

  • resolution (int, default=50000) – Hi-C resolution in bp.

  • dtype (np.dtype, default=np.uint32) – Data type for decoded tiles.

  • use_zstd (bool, default=True) – Use zstd if available, otherwise zlib fallback.

Examples

decode_tile(payload: bytes) → ndarray[source]#

Decode a single compressed tile.

Parameters:

payload (bytes) – Compressed bitstream.

Returns:

Decoded contact matrix tile.

Return type:

np.ndarray

Examples

decode_tiles(payloads: list[bytes]) → ndarray[source]#

Decode multiple tiles into a 4D array.

Parameters:

payloads (list[bytes]) – List of encoded bitstreams.

Returns:

4D array of decoded tiles (n_tile_rows, n_tile_cols, tile_size, tile_size).

Return type:

np.ndarray

Examples