gunz_cm.compressions.cmc_zstd_decoder

Module contents

CMC Transforms + Zstd Decoder for GZCM v3 compression.

Combines CMC’s domain-specific transforms (diagonal transform, binarization) with Zstd entropy coding for faster decode than pure CMC.

Examples

class gunz_cm.compressions.cmc_zstd_decoder.CmcZstdDecoder(tile_size: int = 256, resolution: int = 50000, dtype: ~numpy.dtype = <class 'numpy.uint32'>)

Bases: object

CMC Transforms + Zstd decoder for contact matrix tiles.

Uses Zstd decompression then reverses CMC’s domain-specific transforms.

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.

Examples

decode_tile(payload: bytes) → ndarray

Decode a single compressed tile.

Parameters:

payload (bytes) – Compressed bitstream (shape info + encoded data).

Returns:

Decoded contact matrix tile.

Return type:

np.ndarray

Examples

decode_tiles(payloads: list[bytes]) → ndarray

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