7df6e18265341f87a69fba808aa1f92f8ebca841 markd Wed Apr 15 13:39:42 2026 -0700 move copy of htslib diff --git src/htslib/bgzip.c src/htslib/bgzip.c deleted file mode 100644 index 101d8d0e1e9..00000000000 --- src/htslib/bgzip.c +++ /dev/null @@ -1,297 +0,0 @@ -/* bgzip.c -- Block compression/decompression utility. - - Copyright (C) 2008, 2009 Broad Institute / Massachusetts Institute of Technology - Copyright (C) 2010, 2013-2015 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 notices 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. -*/ - -#include <config.h> - -#include <stdlib.h> -#include <string.h> -#include <stdio.h> -#include <fcntl.h> -#include <unistd.h> -#include <errno.h> -#include <stdarg.h> -#include <getopt.h> -#include <sys/stat.h> -#include "htslib/bgzf.h" -#include "htslib/hts.h" - -static const int WINDOW_SIZE = 64 * 1024; - -static void error(const char *format, ...) -{ - va_list ap; - va_start(ap, format); - vfprintf(stderr, format, ap); - va_end(ap); - exit(EXIT_FAILURE); -} - -static int confirm_overwrite(const char *fn) -{ - int save_errno = errno; - int ret = 0; - - if (isatty(STDIN_FILENO)) { - char c; - fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn); - if (scanf("%c", &c) == 1 && (c == 'Y' || c == 'y')) ret = 1; - } - - errno = save_errno; - return ret; -} - -static int bgzip_main_usage(void) -{ - fprintf(stderr, "\n"); - fprintf(stderr, "Version: %s\n", hts_version()); - fprintf(stderr, "Usage: bgzip [OPTIONS] [FILE] ...\n"); - fprintf(stderr, "Options:\n"); - fprintf(stderr, " -b, --offset INT decompress at virtual file pointer (0-based uncompressed offset)\n"); - fprintf(stderr, " -c, --stdout write on standard output, keep original files unchanged\n"); - fprintf(stderr, " -d, --decompress decompress\n"); - fprintf(stderr, " -f, --force overwrite files without asking\n"); - fprintf(stderr, " -h, --help give this help\n"); - fprintf(stderr, " -i, --index compress and create BGZF index\n"); - fprintf(stderr, " -I, --index-name FILE name of BGZF index file [file.gz.gzi]\n"); - fprintf(stderr, " -r, --reindex (re)index compressed file\n"); - fprintf(stderr, " -s, --size INT decompress INT bytes (uncompressed size)\n"); - fprintf(stderr, " -@, --threads INT number of compression threads to use [1]\n"); - fprintf(stderr, "\n"); - return 1; -} - -int main(int argc, char **argv) -{ - int c, compress, pstdout, is_forced, index = 0, reindex = 0; - BGZF *fp; - void *buffer; - long start, end, size; - char *index_fname = NULL; - int threads = 1; - - static struct option loptions[] = - { - {"help",0,0,'h'}, - {"offset",1,0,'b'}, - {"stdout",0,0,'c'}, - {"decompress",0,0,'d'}, - {"force",0,0,'f'}, - {"index",0,0,'i'}, - {"index-name",1,0,'I'}, - {"reindex",0,0,'r'}, - {"size",1,0,'s'}, - {"threads",1,0,'@'}, - {0,0,0,0} - }; - - compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0; - while((c = getopt_long(argc, argv, "cdh?fb:@:s:iI:r",loptions,NULL)) >= 0){ - switch(c){ - case 'd': compress = 0; break; - case 'c': pstdout = 1; break; - case 'b': start = atol(optarg); compress = 0; pstdout = 1; break; - case 's': size = atol(optarg); pstdout = 1; break; - case 'f': is_forced = 1; break; - case 'i': index = 1; break; - case 'I': index_fname = optarg; break; - case 'r': reindex = 1; compress = 0; break; - case '@': threads = atoi(optarg); break; - case 'h': - case '?': return bgzip_main_usage(); - } - } - if (size >= 0) end = start + size; - if (end >= 0 && end < start) { - fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end); - return 1; - } - if (compress == 1) { - struct stat sbuf; - int f_src = fileno(stdin); - - if ( argc>optind ) - { - if ( stat(argv[optind],&sbuf)<0 ) - { - fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); - return 1; - } - - if ((f_src = open(argv[optind], O_RDONLY)) < 0) { - fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); - return 1; - } - - if (pstdout) - fp = bgzf_open("-", "w"); - else - { - char *name = malloc(strlen(argv[optind]) + 5); - strcpy(name, argv[optind]); - strcat(name, ".gz"); - fp = bgzf_open(name, is_forced? "w" : "wx"); - if (fp == NULL && errno == EEXIST && confirm_overwrite(name)) - fp = bgzf_open(name, "w"); - if (fp == NULL) { - fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno)); - free(name); - return 1; - } - free(name); - } - } - else if (!pstdout && isatty(fileno((FILE *)stdout)) ) - return bgzip_main_usage(); - else if ( index && !index_fname ) - { - fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n"); - return 1; - } - else - fp = bgzf_open("-", "w"); - - if (threads > 1) - bgzf_mt(fp, threads, 256); - - if ( index ) bgzf_index_build_init(fp); - buffer = malloc(WINDOW_SIZE); - while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0) - if (bgzf_write(fp, buffer, c) < 0) error("Could not write %d bytes: Error %d\n", c, fp->errcode); - if ( index ) - { - if ( index_fname ) bgzf_index_dump(fp, index_fname, NULL); - else bgzf_index_dump(fp, argv[optind], ".gz.gzi"); - } - if (bgzf_close(fp) < 0) error("Close failed: Error %d", fp->errcode); - if (argc > optind && !pstdout) unlink(argv[optind]); - free(buffer); - close(f_src); - return 0; - } - else if ( reindex ) - { - if ( argc>optind ) - { - fp = bgzf_open(argv[optind], "r"); - if ( !fp ) error("[bgzip] Could not open file: %s\n", argv[optind]); - } - else - { - if ( !index_fname ) error("[bgzip] Index file name expected when reading from stdin\n"); - fp = bgzf_open("-", "r"); - if ( !fp ) error("[bgzip] Could not read from stdin: %s\n", strerror(errno)); - } - - buffer = malloc(BGZF_BLOCK_SIZE); - bgzf_index_build_init(fp); - int ret; - while ( (ret=bgzf_read(fp, buffer, BGZF_BLOCK_SIZE))>0 ) ; - free(buffer); - if ( ret<0 ) error("Is the file gzipped or bgzipped? The latter is required for indexing.\n"); - - if ( index_fname ) - bgzf_index_dump(fp, index_fname, NULL); - else - bgzf_index_dump(fp, argv[optind], ".gzi"); - - if ( bgzf_close(fp)<0 ) error("Close failed: Error %d\n",fp->errcode); - return 0; - } - else - { - struct stat sbuf; - int f_dst; - - if ( argc>optind ) - { - if ( stat(argv[optind],&sbuf)<0 ) - { - fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]); - return 1; - } - char *name; - int len = strlen(argv[optind]); - if ( strcmp(argv[optind]+len-3,".gz") ) - { - fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]); - return 1; - } - fp = bgzf_open(argv[optind], "r"); - if (fp == NULL) { - fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]); - return 1; - } - - if (pstdout) { - f_dst = fileno(stdout); - } - else { - const int wrflags = O_WRONLY | O_CREAT | O_TRUNC; - name = strdup(argv[optind]); - name[strlen(name) - 3] = '\0'; - f_dst = open(name, is_forced? wrflags : wrflags|O_EXCL, 0666); - if (f_dst < 0 && errno == EEXIST && confirm_overwrite(name)) - f_dst = open(name, wrflags, 0666); - if (f_dst < 0) { - fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno)); - free(name); - return 1; - } - free(name); - } - } - else if (!pstdout && isatty(fileno((FILE *)stdin)) ) - return bgzip_main_usage(); - else - { - f_dst = fileno(stdout); - fp = bgzf_open("-", "r"); - if (fp == NULL) { - fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno)); - return 1; - } - } - buffer = malloc(WINDOW_SIZE); - if ( start>0 ) - { - if ( bgzf_index_load(fp, argv[optind], ".gzi") < 0 ) error("Could not load index: %s.gzi\n", argv[optind]); - if ( bgzf_useek(fp, start, SEEK_SET) < 0 ) error("Could not seek to %d-th (uncompressd) byte\n", start); - } - while (1) { - if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE); - else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start)); - if (c == 0) break; - if (c < 0) error("Could not read %d bytes: Error %d\n", (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start), fp->errcode); - start += c; - if ( write(f_dst, buffer, c) != c ) error("Could not write %d bytes\n", c); - if (end >= 0 && start >= end) break; - } - free(buffer); - if (bgzf_close(fp) < 0) error("Close failed: Error %d\n",fp->errcode); - if (!pstdout) unlink(argv[optind]); - return 0; - } - return 0; -}