/usr/include/io_lib/bgzip.h is in libstaden-read-dev 1.14.9-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 | /*
* Copyright (c) 2016 Genome Research Ltd.
* Author(s): James Bonfield, Rob Davies.
*
* 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 _BGZIP_H_
#define _BGZIP_H_
typedef struct gzi {
uint64_t n;
uint64_t *c_off;
uint64_t *u_off;
} gzi;
int gzi_index_add_block(gzi *idx, uint64_t c_off, uint64_t u_off);
int gzi_index_dump(gzi *idx, const char *bname, const char *suffix);
gzi *gzi_index_init();
gzi *gzi_index_load(const char *fn);
void gzi_index_free(gzi *idx);
uint64_t gzi_load(FILE *fp, gzi *idx, uint64_t ustart, uint64_t uend, char *out);
struct bzi_FILE;
typedef struct bzi_FILE bzi_FILE;
bzi_FILE *bzi_open(const char *path, const char *mode);
void bzi_close(bzi_FILE *zp);
size_t bzi_read(void *ptr, size_t size, size_t nmemb, bzi_FILE *zp);
int bzi_seek(bzi_FILE *zp, off_t offset, int whence);
#endif /* _BGZIP_H_ */
|