bgzf.h

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/* The MIT License

   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
                 2011, 2012 Attractive Chaos <attractor@live.co.uk>
   Copyright (C) 2009, 2013, 2014 Genome Research Ltd

   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
   in the Software without restriction, including without limitation the rights
   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   copies of the Software, and to permit persons to whom the Software is
   furnished to do so, subject to the following conditions:

   The above copyright notice and this permission notice shall be included in
   all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.
*/

/* The BGZF library was originally written by Bob Handsaker from the Broad
 * Institute. It was later improved by the SAMtools developers. */

#ifndef HTSLIB_BGZF_H
#define HTSLIB_BGZF_H

#include <stdint.h>
#include <stdio.h>
#include <zlib.h>
#include <sys/types.h>

#define BGZF_BLOCK_SIZE     0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE
#define BGZF_MAX_BLOCK_SIZE 0x10000

#define BGZF_ERR_ZLIB   1
#define BGZF_ERR_HEADER 2
#define BGZF_ERR_IO     4
#define BGZF_ERR_MISUSE 8

struct hFILE;
struct bgzf_mtaux_t;
typedef struct __bgzidx_t bgzidx_t;

struct BGZF {
    int errcode:16, is_write:2, is_be:2, compress_level:9, is_compressed:2, is_gzip:1;
    int cache_size;
    int block_length, block_offset;
    int64_t block_address, uncompressed_address;
    void *uncompressed_block, *compressed_block;
    void *cache; // a pointer to a hash table
    struct hFILE *fp; // actual file handle
    struct bgzf_mtaux_t *mt; // only used for multi-threading
    bgzidx_t *idx;      // BGZF index
    int idx_build_otf;  // build index on the fly, set by bgzf_index_build_init()
    z_stream *gz_stream;// for gzip-compressed files
};
#ifndef HTS_BGZF_TYPEDEF
typedef struct BGZF BGZF;
#define HTS_BGZF_TYPEDEF
#endif

#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
    size_t l, m;
    char *s;
} kstring_t;
#endif

#ifdef __cplusplus
extern "C" {
#endif

    /******************
     * Basic routines *
     ******************/

    BGZF* bgzf_dopen(int fd, const char *mode);

    #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility

    BGZF* bgzf_open(const char* path, const char *mode);

    BGZF* bgzf_hopen(struct hFILE *fp, const char *mode);

    int bgzf_close(BGZF *fp);

    ssize_t bgzf_read(BGZF *fp, void *data, size_t length);

    ssize_t bgzf_write(BGZF *fp, const void *data, size_t length);

    ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length);

    ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length);

    int bgzf_flush(BGZF *fp);

    #define bgzf_tell(fp) (((fp)->block_address << 16) | ((fp)->block_offset & 0xFFFF))

    int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence);

    int bgzf_check_EOF(BGZF *fp);

     int bgzf_is_bgzf(const char *fn);

    /*********************
     * Advanced routines *
     *********************/

    void bgzf_set_cache_size(BGZF *fp, int size);

    int bgzf_flush_try(BGZF *fp, ssize_t size);

    int bgzf_getc(BGZF *fp);

    int bgzf_getline(BGZF *fp, int delim, kstring_t *str);

    int bgzf_read_block(BGZF *fp);

    int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks);


    /*******************
     * bgzidx routines *
     *******************/

    int bgzf_useek(BGZF *fp, long uoffset, int where);

    long bgzf_utell(BGZF *fp);

    int bgzf_index_build_init(BGZF *fp);

    int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix);

    int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix);

#ifdef __cplusplus
}
#endif

#endif