X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam_view.c;h=113c6c437479237791cee16164d6fbc06cd7af8b;hb=4c2687f34917ab1767b8c5ae60b8aba564d2c95a;hp=1776b8eb586b99b3123b8dffaeb39849179d30cc;hpb=9bd8cd7dd42efa091a9361bb06a29d1bead405ce;p=samtools.git

diff --git a/sam_view.c b/sam_view.c
index 1776b8e..113c6c4 100644
--- a/sam_view.c
+++ b/sam_view.c
@@ -77,16 +77,14 @@ int main_samview(int argc, char *argv[])
 	if (argc == optind) return usage(is_long_help);
 
 	// generate the fn_list if necessary
-	if (fn_list && fn_ref) {
-		fprintf(stderr, "[main_samview] both -t and -T are applied. -T is ignored.\n");
-	} else fn_list = samfaipath(fn_ref);
+	if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref);
 	// open file handlers
 	if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
 		fprintf(stderr, "[main_samview] fail to open file for reading.\n");
 		goto view_end;
 	}
 	if (in->header == 0) {
-		fprintf(stderr, "[main_samview] fail to read SAM header.\n");
+		fprintf(stderr, "[main_samview] fail to read the header.\n");
 		goto view_end;
 	}
 	if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
@@ -142,7 +140,7 @@ static int usage(int is_long_help)
 	fprintf(stderr, "         -S       input is SAM\n");
 	fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
 	fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
-	fprintf(stderr, "         -X       output FLAG in stirng (samtools-C specific)\n");
+	fprintf(stderr, "         -X       output FLAG in string (samtools-C specific)\n");
 	fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
 	fprintf(stderr, "         -T FILE  reference sequence file (force -S) [null]\n");
 	fprintf(stderr, "         -o FILE  output file name [stdout]\n");