htslib-test 1.7-2 / usr / share / htslib-test / cram / cram_codecs.h

/*
Copyright (c) 2012-2013 Genome Research Ltd.
Author: James Bonfield <jkb@sanger.ac.uk>

Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions are met:

   1. Redistributions of source code must retain the above copyright notice, 
this list of conditions and the following disclaimer.

   2. Redistributions in binary form must reproduce the above copyright notice, 
this list of conditions and the following disclaimer in the documentation 
and/or other materials provided with the distribution.

   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
Institute nor the names of its contributors may be used to endorse or promote
products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/

#ifndef _CRAM_ENCODINGS_H_
#define _CRAM_ENCODINGS_H_

#include <inttypes.h>

#ifdef __cplusplus
extern "C" {
#endif

struct cram_codec;

/*
 * Slow but simple huffman decoder to start with.
 * Read a bit at a time, keeping track of {length, value}
 * eg. 1 1 0 1 => {1,1},  {2,3}, {3,6}, {4,13}
 *
 * Keep track of this through the huffman code table.
 * For fast scanning we have an index of where the first code of length X
 * appears.
 */
typedef struct {
    int32_t symbol;
    int32_t p; // next code start value, minus index to codes[]
    int32_t code;
    int32_t len;
} cram_huffman_code;

typedef struct {
    int ncodes;
    cram_huffman_code *codes;
} cram_huffman_decoder;

#define MAX_HUFF 128
typedef struct {
    cram_huffman_code *codes;
    int nvals;
    int val2code[MAX_HUFF+1]; // value to code lookup for small values
} cram_huffman_encoder;

typedef struct {
    int32_t offset;
    int32_t nbits;
} cram_beta_decoder;

typedef struct {
    int32_t offset;
} cram_gamma_decoder;

typedef struct {
    int32_t offset;
    int32_t k;
} cram_subexp_decoder;

typedef struct {
    int32_t content_id;
    enum cram_external_type type;
    cram_block *b;
} cram_external_decoder;

typedef struct {
    struct cram_codec *len_codec;
    struct cram_codec *val_codec;
} cram_byte_array_len_decoder;

typedef struct {
    unsigned char stop;
    int32_t content_id;
    cram_block *b;
} cram_byte_array_stop_decoder;

typedef struct {
    enum cram_encoding len_encoding;
    enum cram_encoding val_encoding;
    void *len_dat;
    void *val_dat;
    struct cram_codec *len_codec;
    struct cram_codec *val_codec;
} cram_byte_array_len_encoder;

/*
 * A generic codec structure.
 */
typedef struct cram_codec {
    enum cram_encoding codec;
    cram_block *out;
    void (*free)(struct cram_codec *codec);
    int (*decode)(cram_slice *slice, struct cram_codec *codec,
		  cram_block *in, char *out, int *out_size);
    int (*encode)(cram_slice *slice, struct cram_codec *codec,
		  char *in, int in_size);
    int (*store)(struct cram_codec *codec, cram_block *b, char *prefix,
		 int version);
    void (*reset)(struct cram_codec *codec); // used between slices in a container

    union {
	cram_huffman_decoder         huffman;
	cram_external_decoder        external;
	cram_beta_decoder            beta;
	cram_gamma_decoder           gamma;
	cram_subexp_decoder          subexp;
	cram_byte_array_len_decoder  byte_array_len;
	cram_byte_array_stop_decoder byte_array_stop;

	cram_huffman_encoder         e_huffman;
	cram_external_decoder        e_external;
	cram_byte_array_stop_decoder e_byte_array_stop;
	cram_byte_array_len_encoder  e_byte_array_len;
	cram_beta_decoder            e_beta;
    };
} cram_codec;

const char *cram_encoding2str(enum cram_encoding t);

cram_codec *cram_decoder_init(enum cram_encoding codec, char *data, int size,
			      enum cram_external_type option,
			      int version);
cram_codec *cram_encoder_init(enum cram_encoding codec, cram_stats *st,
			      enum cram_external_type option, void *dat,
			      int version);

//int cram_decode(void *codes, char *in, int in_size, char *out, int *out_size);
//void cram_decoder_free(void *codes);

//#define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, (--b->bit == -1) && (b->bit = 7, b->byte++))

#define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (--b->bit<0), b->bit&=7)

/*
 * Check that enough bits are left in a block to satisy a bit-based decoder.
 * Return  0 if there are enough
 *         1 if not.
 */

static inline int cram_not_enough_bits(cram_block *blk, int nbits) {
    if (nbits < 0 ||
	(blk->byte >= blk->uncomp_size && nbits > 0) ||
	(blk->uncomp_size - blk->byte <= INT32_MAX / 8 + 1 &&
	 (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
        return 1;
    }
    return 0;
}

/*
 * Returns the content_id used by this codec, also in id2 if byte_array_len.
 * Returns -1 for the CORE block and -2 for unneeded.
 * id2 is only filled out for BYTE_ARRAY_LEN which uses 2 codecs.
 */
int cram_codec_to_id(cram_codec *c, int *id2);

/*
 * cram_codec structures are specialised for decoding or encoding.
 * Unfortunately this makes turning a decoder into an encoder (such as
 * when transcoding files) problematic.
 *
 * This function converts a cram decoder codec into an encoder version
 * in-place (ie it modifiers the codec itself).
 *
 * Returns 0 on success;
 *        -1 on failure.
 */
int cram_codec_decoder2encoder(cram_fd *fd, cram_codec *c);

#ifdef __cplusplus
}
#endif

#endif /* _CRAM_ENCODINGS_H_ */