* samtools-0.1.3-14 (r262)

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index cefac2f4835e84c4d6846862b85dc59b9032badf..f070b32a6f671c995be3733e6c9d0f1fbe166473 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -26,15 +26,16 @@ int main_samview(int argc, char *argv[])
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "bt:hHo:q:f:F:")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:")) >= 0) {
                switch (c) {
+               case 'S': is_bamin = 0; break;
                case 'b': strcat(out_mode, "b"); break;
                case 't': fn_list = strdup(optarg); is_bamin = 0; break;
                case 'h': is_header = 1; break;
                case 'H': is_header_only = 1; break;
                case 'o': fn_out = strdup(optarg); break;
                case 'f': g_flag_on = strtol(optarg, 0, 0); break;
-               case 'F': g_flag_on = strtol(optarg, 0, 0); break;
+               case 'F': g_flag_off = strtol(optarg, 0, 0); break;
                case 'q': g_min_mapQ = atoi(optarg); break;
                default: return usage();
                }
@@ -98,7 +99,8 @@ static int usage()
        fprintf(stderr, "Options: -b       output BAM\n");
        fprintf(stderr, "         -h       print header for the SAM output\n");
        fprintf(stderr, "         -H       print header only (no alignments)\n");
-       fprintf(stderr, "         -t FILE  list of reference names and lengths, assuming SAM input [null]\n");
+       fprintf(stderr, "         -S       input is SAM\n");
+       fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
        fprintf(stderr, "         -o FILE  output file name [stdout]\n");
        fprintf(stderr, "         -f INT   required flag, 0 for unset [0]\n");
        fprintf(stderr, "         -F INT   filtering flag, 0 for unset [0]\n");