X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bgzip.c;h=ebcafa20651fd2b3a9863bfe38dc590497099671;hp=ac2a98ea35eb2503d94652918054575b341f5cc1;hb=HEAD;hpb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351

diff --git a/bgzip.c b/bgzip.c
index ac2a98e..ebcafa2 100644
--- a/bgzip.c
+++ b/bgzip.c
@@ -27,22 +27,24 @@
 #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)
@@ -51,129 +53,154 @@ static int write_open(const char *fn, int is_forced)
 	char c;
 	if (!is_forced) {
 		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
-			printf("bgzip: %s already exists; do you wish to overwrite (y or n)? ", fn);
+			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, 0666)) < 0) {
-			fprintf(stderr, "bgzip: %s: Fail to write\n", fn);
+			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;
 	}
 }
-