X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=bgzip.c;h=5429a22cac00ffa8c437ccffc75f6143e8eed553;hp=381ebc5d86190d79a808b911e7a15c35baa00bcb;hb=HEAD;hpb=bc08e6c2f34c1367d0fe75dd19cedccfab881229

diff --git a/bgzip.c b/bgzip.c
index 381ebc5..5429a22 100644
--- 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);