#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()
{
- printf("\n");
- printf("Usage: bgzip [options] [file] ...\n\n");
- printf("Options: -c write on standard output, keep original files unchanged\n");
- printf(" -d decompress\n");
- // printf(" -l list compressed file contents\n");
- printf(" -b INT decompress at virtual file pointer INT\n");
- printf(" -s INT decompress INT bytes in the uncompressed file\n");
- printf(" -h give this help\n");
- printf("\n");
- return 0;
+ 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, 0644)) < 0 && errno == EEXIST) {
- printf("bgzip: %s already exists; do you wish to overwrite (y or n)? ", fn);
+ 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') {
- printf("bgzip: not overwritten\n");
+ fprintf(stderr, "[bgzip] not overwritten\n");
exit(1);
}
}
}
if (fd < 0) {
- if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0644)) < 0) {
- fprintf(stderr, "bgzip: %s: Fail to write\n", fn);
+ 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)
+static void fail(BGZF* fp)
{
- printf("Error: %s\n", fp->error);
+ fprintf(stderr, "Error: %s\n", fp->error);
exit(1);
}
int main(int argc, char **argv)
{
int c, compress, pstdout, is_forced;
- BGZF *rz;
+ 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, "cdlhfb:s:")) >= 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 'l': compress = 2; 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, " -- Illegal region: [%ld, %ld] --\n", start, end);
+ if (end >= 0 && end < start) {
+ fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);
return 1;
}
- if(compress == 1){
- int f_src, f_dst = -1;
- if(argc > optind){
- if((f_src = open(argv[optind], O_RDONLY)) < 0){
- fprintf(stderr, " -- Cannot open file: %s --\n", argv[optind]);
+ 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){
+
+ if (pstdout)
f_dst = fileno(stdout);
- } else {
- char *name = malloc(sizeof(strlen(argv[optind]) + 5));
+ 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){
- f_src = fileno(stdin);
- f_dst = fileno(stdout);
- } else return bgzip_main_usage();
- rz = bgzf_fdopen(f_dst, "w");
+ }
+ 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(rz, buffer, c) < 0) {
- fail(rz);
- }
- }
- // f_dst will be closed here
- if (bgzf_close(rz) < 0) {
- fail(rz);
- }
- if (argc > optind) unlink(argv[optind]);
+ 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 && !pstdout) unlink(argv[optind]);
free(buffer);
close(f_src);
return 0;
} else {
- if(argc <= optind) return bgzip_main_usage();
- int f_dst;
- if (argc > optind && !pstdout) {
- char *name;
- if (strstr(argv[optind], ".gz") - argv[optind] != strlen(argv[optind]) - 3) {
- printf("bgzip: %s: unknown suffix -- ignored\n", argv[optind]);
- return 1;
- }
- name = strdup(argv[optind]);
- name[strlen(name) - 3] = '\0';
- f_dst = write_open(name, is_forced);
- free(name);
- } else f_dst = fileno(stdout);
- rz = bgzf_open(argv[optind], "r");
- if (rz == NULL) {
- printf("Could not open file: %s\n", argv[optind]);
- return 1;
- }
- buffer = malloc(WINDOW_SIZE);
- if (bgzf_seek(rz, start, SEEK_SET) < 0) {
- fail(rz);
- }
- while(1){
- if(end < 0) c = bgzf_read(rz, buffer, WINDOW_SIZE);
- else c = bgzf_read(rz, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
- if(c == 0) break;
- if (c < 0) fail(rz);
- start += c;
- write(f_dst, buffer, c);
- if(end >= 0 && start >= end) break;
- }
- free(buffer);
- if (bgzf_close(rz) < 0) {
- fail(rz);
- }
- if (!pstdout) unlink(argv[optind]);
+ 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 {
+ 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 / samtools.git / blobdiff