diff options
Diffstat (limited to 'debian/vendor-h2o/deps/klib/bgzf.h')
| -rw-r--r-- | debian/vendor-h2o/deps/klib/bgzf.h | 196 |
1 files changed, 0 insertions, 196 deletions
diff --git a/debian/vendor-h2o/deps/klib/bgzf.h b/debian/vendor-h2o/deps/klib/bgzf.h deleted file mode 100644 index 29fe0e5..0000000 --- a/debian/vendor-h2o/deps/klib/bgzf.h +++ /dev/null @@ -1,196 +0,0 @@ -/* The MIT License - - Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology - 2011 Attractive Chaos <attractor@live.co.uk> - - 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 __BGZF_H -#define __BGZF_H - -#include <stdint.h> -#include <stdio.h> -#include <zlib.h> - -#define BGZF_BLOCK_SIZE 0x10000 -#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 - -typedef struct { - int open_mode:8, compress_level:8, errcode:16; - int cache_size; - int block_length, block_offset; - int64_t block_address; - void *uncompressed_block, *compressed_block; - void *cache; // a pointer to a hash table - void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading -} BGZF; - -#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 * - ******************/ - - /** - * Open an existing file descriptor for reading or writing. - * - * @param fd file descriptor - * @param mode mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies - * the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored. - * @return BGZF file handler; 0 on error - */ - BGZF* bgzf_dopen(int fd, const char *mode); - - #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility - - /** - * Open the specified file for reading or writing. - */ - BGZF* bgzf_open(const char* path, const char *mode); - - /** - * Close the BGZF and free all associated resources. - * - * @param fp BGZF file handler - * @return 0 on success and -1 on error - */ - int bgzf_close(BGZF *fp); - - /** - * Read up to _length_ bytes from the file storing into _data_. - * - * @param fp BGZF file handler - * @param data data array to read into - * @param length size of data to read - * @return number of bytes actually read; 0 on end-of-file and -1 on error - */ - ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length); - - /** - * Write _length_ bytes from _data_ to the file. - * - * @param fp BGZF file handler - * @param data data array to write - * @param length size of data to write - * @return number of bytes actually written; -1 on error - */ - ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length); - - /** - * Write the data in the buffer to the file. - */ - int bgzf_flush(BGZF *fp); - - /** - * Return a virtual file pointer to the current location in the file. - * No interpetation of the value should be made, other than a subsequent - * call to bgzf_seek can be used to position the file at the same point. - * Return value is non-negative on success. - */ - #define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF)) - - /** - * Set the file to read from the location specified by _pos_. - * - * @param fp BGZF file handler - * @param pos virtual file offset returned by bgzf_tell() - * @param whence must be SEEK_SET - * @return 0 on success and -1 on error - */ - int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence); - - /** - * Check if the BGZF end-of-file (EOF) marker is present - * - * @param fp BGZF file handler opened for reading - * @return 1 if EOF is present; 0 if not or on I/O error - */ - int bgzf_check_EOF(BGZF *fp); - - /** - * Check if a file is in the BGZF format - * - * @param fn file name - * @return 1 if _fn_ is BGZF; 0 if not or on I/O error - */ - int bgzf_is_bgzf(const char *fn); - - /********************* - * Advanced routines * - *********************/ - - /** - * Set the cache size. Only effective when compiled with -DBGZF_CACHE. - * - * @param fp BGZF file handler - * @param size size of cache in bytes; 0 to disable caching (default) - */ - void bgzf_set_cache_size(BGZF *fp, int size); - - /** - * Flush the file if the remaining buffer size is smaller than _size_ - */ - int bgzf_flush_try(BGZF *fp, ssize_t size); - - /** - * Read one byte from a BGZF file. It is faster than bgzf_read() - * @param fp BGZF file handler - * @return byte read; -1 on end-of-file or error - */ - int bgzf_getc(BGZF *fp); - - /** - * Read one line from a BGZF file. It is faster than bgzf_getc() - * - * @param fp BGZF file handler - * @param delim delimitor - * @param str string to write to; must be initialized - * @return length of the string; 0 on end-of-file; negative on error - */ - int bgzf_getline(BGZF *fp, int delim, kstring_t *str); - - /** - * Read the next BGZF block. - */ - int bgzf_read_block(BGZF *fp); - -#ifdef __cplusplus -} -#endif - -#endif |