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Diffstat (limited to '')
| -rw-r--r-- | web/server/h2o/libh2o/deps/klib/bgzf.h | 196 |
1 files changed, 196 insertions, 0 deletions
diff --git a/web/server/h2o/libh2o/deps/klib/bgzf.h b/web/server/h2o/libh2o/deps/klib/bgzf.h new file mode 100644 index 00000000..29fe0e5d --- /dev/null +++ b/web/server/h2o/libh2o/deps/klib/bgzf.h @@ -0,0 +1,196 @@ +/* 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 |