gunz_cm.compressions.cmc_zstd_encoder#

Module contents#

CMC Transforms + Zstd Encoder 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_encoder.CmcZstdEncoder(tile_size: int = 256, resolution: int = 50000, level: int = 3)[source]#

CMC Transforms + Zstd encoder for contact matrix tiles.

Uses CMC’s domain-specific transforms (diagonal transform, binarization) with Zstd entropy coding for better compression and faster decode.

Parameters:

tile_size (int, default=256) – Tile size for block processing.
resolution (int, default=50000) – Hi-C resolution in bp.
level (int, default=3) – Compression level (1-22 for zstd, 1-9 for zlib fallback).

Examples

encode_tile(mat: ndarray) → bytes[source]#

Encode a single contact matrix tile.

Parameters:: mat (np.ndarray) – 2D contact matrix tile (upper triangular).
Returns:: Compressed bitstream (shape info + encoded data).
Return type:: bytes

Examples

encode_tiles(tiles: ndarray) → list[bytes][source]#

Encode multiple tiles.

Parameters:: tiles (np.ndarray) – 4D array of shape (n_tile_rows, n_tile_cols, tile_size, tile_size).
Returns:: List of encoded bitstreams, one per tile.
Return type:: list[bytes]

Examples

get_compression_info() → dict[source]#

Return compression metadata.

Examples