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[GalaxyCodeBases.git] / c_cpp / lib / klib / bgzf.h
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1 /* The MIT License
3 Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
4 2011 Attractive Chaos <attractor@live.co.uk>
6 Permission is hereby granted, free of charge, to any person obtaining a copy
7 of this software and associated documentation files (the "Software"), to deal
8 in the Software without restriction, including without limitation the rights
9 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
10 copies of the Software, and to permit persons to whom the Software is
11 furnished to do so, subject to the following conditions:
13 The above copyright notice and this permission notice shall be included in
14 all copies or substantial portions of the Software.
16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
17 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
18 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
19 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
20 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
21 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
22 THE SOFTWARE.
25 /* The BGZF library was originally written by Bob Handsaker from the Broad
26 * Institute. It was later improved by the SAMtools developers. */
28 #ifndef __BGZF_H
29 #define __BGZF_H
31 #include <stdint.h>
32 #include <stdio.h>
33 #include <zlib.h>
35 #define BGZF_BLOCK_SIZE 0x10000
36 #define BGZF_MAX_BLOCK_SIZE 0x10000
38 #define BGZF_ERR_ZLIB 1
39 #define BGZF_ERR_HEADER 2
40 #define BGZF_ERR_IO 4
41 #define BGZF_ERR_MISUSE 8
43 typedef struct {
44 int open_mode:8, compress_level:8, errcode:16;
45 int cache_size;
46 int block_length, block_offset;
47 int64_t block_address;
48 void *uncompressed_block, *compressed_block;
49 void *cache; // a pointer to a hash table
50 void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading
51 } BGZF;
53 #ifndef KSTRING_T
54 #define KSTRING_T kstring_t
55 typedef struct __kstring_t {
56 size_t l, m;
57 char *s;
58 } kstring_t;
59 #endif
61 #ifdef __cplusplus
62 extern "C" {
63 #endif
65 /******************
66 * Basic routines *
67 ******************/
69 /**
70 * Open an existing file descriptor for reading or writing.
72 * @param fd file descriptor
73 * @param mode mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies
74 * the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored.
75 * @return BGZF file handler; 0 on error
77 BGZF* bgzf_dopen(int fd, const char *mode);
79 #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility
81 /**
82 * Open the specified file for reading or writing.
84 BGZF* bgzf_open(const char* path, const char *mode);
86 /**
87 * Close the BGZF and free all associated resources.
89 * @param fp BGZF file handler
90 * @return 0 on success and -1 on error
92 int bgzf_close(BGZF *fp);
94 /**
95 * Read up to _length_ bytes from the file storing into _data_.
97 * @param fp BGZF file handler
98 * @param data data array to read into
99 * @param length size of data to read
100 * @return number of bytes actually read; 0 on end-of-file and -1 on error
102 ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length);
105 * Write _length_ bytes from _data_ to the file.
107 * @param fp BGZF file handler
108 * @param data data array to write
109 * @param length size of data to write
110 * @return number of bytes actually written; -1 on error
112 ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length);
115 * Write the data in the buffer to the file.
117 int bgzf_flush(BGZF *fp);
120 * Return a virtual file pointer to the current location in the file.
121 * No interpetation of the value should be made, other than a subsequent
122 * call to bgzf_seek can be used to position the file at the same point.
123 * Return value is non-negative on success.
125 #define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
128 * Set the file to read from the location specified by _pos_.
130 * @param fp BGZF file handler
131 * @param pos virtual file offset returned by bgzf_tell()
132 * @param whence must be SEEK_SET
133 * @return 0 on success and -1 on error
135 int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence);
138 * Check if the BGZF end-of-file (EOF) marker is present
140 * @param fp BGZF file handler opened for reading
141 * @return 1 if EOF is present; 0 if not or on I/O error
143 int bgzf_check_EOF(BGZF *fp);
146 * Check if a file is in the BGZF format
148 * @param fn file name
149 * @return 1 if _fn_ is BGZF; 0 if not or on I/O error
151 int bgzf_is_bgzf(const char *fn);
153 /*********************
154 * Advanced routines *
155 *********************/
158 * Set the cache size. Only effective when compiled with -DBGZF_CACHE.
160 * @param fp BGZF file handler
161 * @param size size of cache in bytes; 0 to disable caching (default)
163 void bgzf_set_cache_size(BGZF *fp, int size);
166 * Flush the file if the remaining buffer size is smaller than _size_
168 int bgzf_flush_try(BGZF *fp, ssize_t size);
171 * Read one byte from a BGZF file. It is faster than bgzf_read()
172 * @param fp BGZF file handler
173 * @return byte read; -1 on end-of-file or error
175 int bgzf_getc(BGZF *fp);
178 * Read one line from a BGZF file. It is faster than bgzf_getc()
180 * @param fp BGZF file handler
181 * @param delim delimitor
182 * @param str string to write to; must be initialized
183 * @return length of the string; 0 on end-of-file; negative on error
185 int bgzf_getline(BGZF *fp, int delim, kstring_t *str);
188 * Read the next BGZF block.
190 int bgzf_read_block(BGZF *fp);
192 #ifdef __cplusplus
194 #endif
196 #endif