* samtools-0.1.5-17 (r416)

[samtools.git] / sam_view.c

diff --git a/sam_view.c b/sam_view.c
index f253dbf7e65ecffd401a1dfcb854f93ed7463c71..9af2194bc90f9c8b6fc47445c94279ccb514afb8 100644 (file)
--- a/sam_view.c
+++ b/sam_view.c
@@ -35,13 +35,14 @@ static int usage(void);
 
 int main_samview(int argc, char *argv[])
 {
-       int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, is_hex = 0;
+       int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
+       int of_type = BAM_OFDEC;
        samfile_t *in = 0, *out = 0;
        char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
 
        /* parse command-line options */
        strcpy(in_mode, "r"); strcpy(out_mode, "w");
-       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:x")) >= 0) {
+       while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX")) >= 0) {
                switch (c) {
                case 'S': is_bamin = 0; break;
                case 'b': is_bamout = 1; break;
@@ -55,17 +56,21 @@ int main_samview(int argc, char *argv[])
                case 'u': is_uncompressed = 1; break;
                case 'l': g_library = strdup(optarg); break;
                case 'r': g_rg = strdup(optarg); break;
-               case 'x': is_hex = 1; break;
+               case 'x': of_type = BAM_OFHEX; break;
+               case 'X': of_type = BAM_OFSTR; break;
                default: return usage();
                }
        }
        if (is_uncompressed) is_bamout = 1;
        if (is_header_only) is_header = 1;
        if (is_bamout) strcat(out_mode, "b");
+       else {
+               if (of_type == BAM_OFHEX) strcat(out_mode, "x");
+               else if (of_type == BAM_OFSTR) strcat(out_mode, "X");
+       }
        if (is_bamin) strcat(in_mode, "b");
        if (is_header) strcat(out_mode, "h");
        if (is_uncompressed) strcat(out_mode, "u");
-       if (is_hex && !is_bamout) strcat(out_mode, "x");
        if (argc == optind) return usage();
 
        // open file handlers
@@ -126,6 +131,7 @@ static int usage()
        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, "         -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");