+++ /dev/null
-/* The MIT License
-
- Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
-
- 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.
-*/
-
-#include <stdlib.h>
-#include <string.h>
-#include <stdio.h>
-#include <fcntl.h>
-#include <unistd.h>
-#include <errno.h>
-#include <sys/select.h>
-#include <sys/stat.h>
-#include "bgzf.h"
-
-static const int WINDOW_SIZE = 64 * 1024;
-
-static int bgzip_main_usage()
-{
- fprintf(stderr, "\n");
- fprintf(stderr, "Usage: bgzip [options] [file] ...\n\n");
- fprintf(stderr, "Options: -c write on standard output, keep original files unchanged\n");
- fprintf(stderr, " -d decompress\n");
- fprintf(stderr, " -f overwrite files without asking\n");
- fprintf(stderr, " -b INT decompress at virtual file pointer INT\n");
- fprintf(stderr, " -s INT decompress INT bytes in the uncompressed file\n");
- fprintf(stderr, " -h give this help\n");
- fprintf(stderr, "\n");
- return 1;
-}
-
-static int write_open(const char *fn, int is_forced)
-{
- int fd = -1;
- char c;
- if (!is_forced) {
- if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
- fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
- scanf("%c", &c);
- if (c != 'Y' && c != 'y') {
- fprintf(stderr, "[bgzip] not overwritten\n");
- exit(1);
- }
- }
- }
- if (fd < 0) {
- if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
- fprintf(stderr, "[bgzip] %s: Fail to write\n", fn);
- exit(1);
- }
- }
- return fd;
-}
-
-static void fail(BGZF* fp)
-{
- fprintf(stderr, "Error: %s\n", fp->error);
- exit(1);
-}
-
-int main(int argc, char **argv)
-{
- int c, compress, pstdout, is_forced;
- BGZF *fp;
- void *buffer;
- long start, end, size;
-
- compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
- while((c = getopt(argc, argv, "cdhfb:s:")) >= 0){
- switch(c){
- case 'h': return bgzip_main_usage();
- case 'd': compress = 0; break;
- case 'c': pstdout = 1; break;
- case 'b': start = atol(optarg); break;
- case 's': size = atol(optarg); break;
- case 'f': is_forced = 1; break;
- }
- }
- 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);
- int f_dst = fileno(stdout);
-
- 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)
- f_dst = fileno(stdout);
- else
- {
- char *name = malloc(strlen(argv[optind]) + 5);
- strcpy(name, argv[optind]);
- strcat(name, ".gz");
- f_dst = write_open(name, is_forced);
- if (f_dst < 0) return 1;
- free(name);
- }
- }
- else if (!pstdout && isatty(fileno((FILE *)stdout)) )
- return bgzip_main_usage();
-
- fp = bgzf_fdopen(f_dst, "w");
- buffer = malloc(WINDOW_SIZE);
- while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
- if (bgzf_write(fp, buffer, c) < 0) fail(fp);
- // f_dst will be closed here
- if (bgzf_close(fp) < 0) fail(fp);
- if (argc > optind) unlink(argv[optind]);
- free(buffer);
- close(f_src);
- 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;
- }
-
- name = strdup(argv[optind]);
- name[strlen(name) - 3] = '\0';
- f_dst = write_open(name, is_forced);
- free(name);
- }
- else if (!pstdout && isatty(fileno((FILE *)stdin)) )
- return bgzip_main_usage();
- else
- {
- f_dst = fileno(stdout);
- fp = bgzf_fdopen(fileno(stdin), "r");
- if (fp == NULL) {
- fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
- return 1;
- }
- }
- buffer = malloc(WINDOW_SIZE);
- if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp);
- 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) fail(fp);
- start += c;
- write(f_dst, buffer, c);
- if (end >= 0 && start >= end) break;
- }
- free(buffer);
- if (bgzf_close(fp) < 0) fail(fp);
- if (!pstdout) unlink(argv[optind]);
- return 0;
- }
-}
projects / pysam.git / blobdiff