Changelog entry marking the package released.

[tabix.git] / bgzip.c

diff --git a/bgzip.c b/bgzip.c
index 381ebc5d86190d79a808b911e7a15c35baa00bcb..5429a22cac00ffa8c437ccffc75f6143e8eed553 100644 (file)
--- a/bgzip.c
+++ b/bgzip.c
@@ -28,26 +28,18 @@
 #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 is_ready(int fd)
-{
-       fd_set fdset;
-       struct timeval timeout;
-       FD_ZERO(&fdset);
-       FD_SET(fd, &fdset);
-       timeout.tv_sec = 0; timeout.tv_usec = 100000;
-       return select(1, &fdset, NULL, NULL, &timeout) == 1 ? 1 : 0;
-}
-
 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");
@@ -80,7 +72,7 @@ static int write_open(const char *fn, int is_forced)
 
 static void fail(BGZF* fp)
 {
-    fprintf(stderr, "Error: %s\n", fp->error);
+    fprintf(stderr, "Error: %d\n", fp->errcode);
     exit(1);
 }
 
@@ -108,57 +100,92 @@ int main(int argc, char **argv)
                return 1;
        }
        if (compress == 1) {
-               int f_src, f_dst = -1;
-               if (is_ready(fileno(stdin))) pstdout = 1;
-               if (argc > optind && !pstdout) {
+               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] Cannot open file: %s\n", argv[optind]);
+                               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();
-               fp = bgzf_fdopen(f_dst, "w");
+               }
+               else if (!pstdout && isatty(fileno((FILE *)stdout)) )
+                       return bgzip_main_usage();
+
+               fp = bgzf_dopen(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]);
+               if (argc > optind && !pstdout) unlink(argv[optind]);
                free(buffer);
                close(f_src);
                return 0;
        } else {
-               int f_dst, is_stdin = 0;
-               if (argc == optind) pstdout = 1;
-               if (is_ready(fileno(stdin))) is_stdin = 1;
-               if (argc <= optind && !is_stdin) return bgzip_main_usage();
-               if (argc > optind && !pstdout) {
+               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;
-                       if (strstr(argv[optind], ".gz") - argv[optind] != strlen(argv[optind]) - 3) {
+                       int len = strlen(argv[optind]);
+                       if ( strcmp(argv[optind]+len-3,".gz") )
+                       {
                                fprintf(stderr, "[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);
-               fp = (argc == optind)? bgzf_fdopen(fileno(stdin), "r") : bgzf_open(argv[optind], "r");
-               if (fp == NULL) {
-                       fprintf(stderr, "[bgzip] Could not open file: %s\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_dopen(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);