X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=bgzip.c;h=5429a22cac00ffa8c437ccffc75f6143e8eed553;hp=d144632c64a1f7b8f7ce2d060c49a680e50f7915;hb=HEAD;hpb=c70c92b7a385548d8e670638a93a083401f49e4d

diff --git a/bgzip.c b/bgzip.c
index d144632..5429a22 100644
--- a/bgzip.c
+++ b/bgzip.c
@@ -72,7 +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);
 }
 
@@ -132,13 +132,13 @@ int main(int argc, char **argv)
 		else if (!pstdout && isatty(fileno((FILE *)stdout)) )
 			return bgzip_main_usage();
 
-		fp = bgzf_fdopen(f_dst, "w");
+		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;
@@ -166,17 +166,22 @@ int main(int argc, char **argv)
 				return 1;
 			}
 
-			name = strdup(argv[optind]);
-			name[strlen(name) - 3] = '\0';
-			f_dst = write_open(name, is_forced);
-			free(name);
+			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");
+			fp = bgzf_dopen(fileno(stdin), "r");
 			if (fp == NULL) {
 				fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
 				return 1;