/usr/include/io_lib/cram

/*
 * Copyright (c) 2013, 2014, 2015 Genome Research Ltd.
 * Author(s): James Bonfield
 * 
 * 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.
 */

/*
 * Author: James Bonfield, Wellcome Trust Sanger Institute. 2013
 */

#ifndef _CRAM_ENCODINGS_H_
#define _CRAM_ENCODINGS_H_

#ifdef __cplusplus
extern "C" {
#endif

#include <inttypes.h>

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_ */
libstaden-read-dev 1.14.9-4 / usr / include / io_lib / cram_codecs.h
