7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/htslib/bgzf.h src/htslib/htslib/bgzf.h deleted file mode 100644 index 207075ecfe0..00000000000 --- src/htslib/htslib/bgzf.h +++ /dev/null @@ -1,329 +0,0 @@ -/* 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> - -#ifdef __cplusplus -extern "C" { -#endif - -#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 { - unsigned errcode:16, is_write:2, is_be:2; - signed compress_level:9; - unsigned 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 - - /****************** - * Basic routines * - ******************/ - - /** - * Open an existing file descriptor for reading or writing. - * - * @param fd file descriptor - * @param mode mode matching /[rwag][u0-9]+/: 'r' for reading, 'w' for - * writing, 'a' for appending, 'g' for gzip rather than BGZF - * compression (with 'w' only), and digit specifies the zlib - * compression level. - * Note that there is a distinction between 'u' and '0': the - * first yields plain uncompressed output whereas the latter - * outputs uncompressed data wrapped in the zlib format. - * @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); - - /** - * Open an existing hFILE stream for reading or writing. - */ - BGZF* bgzf_hopen(struct hFILE *fp, 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, size_t length); - - /** - * Write _length_ bytes from _data_ to the file. If no I/O errors occur, - * the complete _length_ bytes will be written (or queued for writing). - * - * @param fp BGZF file handler - * @param data data array to write - * @param length size of data to write - * @return number of bytes written (i.e., _length_); negative on error - */ - ssize_t bgzf_write(BGZF *fp, const void *data, size_t length); - - /** - * Read up to _length_ bytes directly from the underlying stream without - * decompressing. Bypasses BGZF blocking, so must be used with care in - * specialised circumstances only. - * - * @param fp BGZF file handler - * @param data data array to read into - * @param length number of raw bytes to read - * @return number of bytes actually read; 0 on end-of-file and -1 on error - */ - ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length); - - /** - * Write _length_ bytes directly to the underlying stream without - * compressing. Bypasses BGZF blocking, so must be used with care - * in specialised circumstances only. - * - * @param fp BGZF file handler - * @param data data array to write - * @param length number of raw bytes to write - * @return number of bytes actually written; -1 on error - */ - ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_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 the EOF marker is present and correct; - * 2 if it can't be checked, e.g., because fp isn't seekable; - * 0 if the EOF marker is absent; - * -1 (with errno set) on 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_ - * @return 0 if flushing succeeded or was not needed; negative on error - */ - 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); - - /** - * Enable multi-threading (only effective on writing and when the - * library was compiled with -DBGZF_MT) - * - * @param fp BGZF file handler; must be opened for writing - * @param n_threads #threads used for writing - * @param n_sub_blks #blocks processed by each thread; a value 64-256 is recommended - */ - int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks); - - /** - * Compress a single BGZF block. - * - * @param dst output buffer (must have size >= BGZF_MAX_BLOCK_SIZE) - * @param dlen size of output buffer; updated on return to the number - * of bytes actually written to dst - * @param src buffer to be compressed - * @param slen size of data to compress (must be <= BGZF_BLOCK_SIZE) - * @param level compression level - * @return 0 on success and negative on error - */ - int bgzf_compress(void *dst, size_t *dlen, const void *src, size_t slen, int level); - - /******************* - * bgzidx routines * - *******************/ - - /** - * Position BGZF at the uncompressed offset - * - * @param fp BGZF file handler; must be opened for reading - * @param uoffset file offset in the uncompressed data - * @param where SEEK_SET supported atm - * - * Returns 0 on success and -1 on error. - */ - int bgzf_useek(BGZF *fp, long uoffset, int where); - - /** - * Position in uncompressed BGZF - * - * @param fp BGZF file handler; must be opened for reading - * - * Returns the current offset on success and -1 on error. - */ - long bgzf_utell(BGZF *fp); - - /** - * Tell BGZF to build index while compressing. - * - * @param fp BGZF file handler; can be opened for reading or writing. - * - * Returns 0 on success and -1 on error. - */ - int bgzf_index_build_init(BGZF *fp); - - /** - * Load BGZF index - * - * @param fp BGZF file handler - * @param bname base name - * @param suffix suffix to add to bname (can be NULL) - * - * Returns 0 on success and -1 on error. - */ - int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix); - - /** - * Save BGZF index - * - * @param fp BGZF file handler - * @param bname base name - * @param suffix suffix to add to bname (can be NULL) - * - * Returns 0 on success and -1 on error. - */ - int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix); - -#ifdef __cplusplus -} -#endif - -#endif