int main_addreplacerg(int argc, char** argv)
{
parsed_opts_t* opts = NULL;
state_t* state = NULL;
if (!parse_args(argc, argv, &opts)) goto error;
if (opts == NULL) return EXIT_SUCCESS; // Not an error but user doesn't want us to proceed
if (!opts || !init(opts, &state)) goto error;
if (!readgroupise(state)) goto error;
cleanup_opts(opts);
cleanup_state(state);
return EXIT_SUCCESS;
error:
cleanup_opts(opts);
cleanup_state(state);
return EXIT_FAILURE;
}
int main_split(int argc, char** argv)
{
int ret = 1;
parsed_opts_t* opts = parse_args(argc, argv);
if (!opts ) goto cleanup_opts;
state_t* status = init(opts);
if (!status) goto cleanup_opts;
if (split(status)) ret = 0;
cleanup_state(status);
cleanup_opts:
cleanup_opts(opts);
return ret;
}
static bool parse_args(int argc, char** argv, parsed_opts_t** opts)
{
*opts = NULL;
int n;
if (argc == 1) { usage(stdout); return true; }
parsed_opts_t* retval = calloc(1, sizeof(parsed_opts_t));
if (! retval ) {
fprintf(stderr, "[%s] Out of memory allocating parsed_opts_t\n", __func__);
return false;
}
// Set defaults
retval->mode = overwrite_all;
sam_global_args_init(&retval->ga);
static const struct option lopts[] = {
SAM_OPT_GLOBAL_OPTIONS(0, 0, 'O', 0, 0),
{ NULL, 0, NULL, 0 }
};
kstring_t rg_line = {0,0,NULL};
while ((n = getopt_long(argc, argv, "r:R:m:o:O:l:h", lopts, NULL)) >= 0) {
switch (n) {
case 'r':
// Are we adding to existing rg line?
if (ks_len(&rg_line) == 0) {
if (strlen(optarg)<3 || (optarg[0] != '@' && optarg[1] != 'R' && optarg[2] != 'G')) {
kputs("@RG\t", &rg_line);
}
} else {
kputs("\t", &rg_line);
}
kputs(optarg, &rg_line);
break;
case 'R':
retval->rg_id = strdup(optarg);
break;
case 'm': {
if (strcmp(optarg, "overwrite_all") == 0) {
retval->mode = overwrite_all;
} else if (strcmp(optarg, "orphan_only") == 0) {
retval->mode = orphan_only;
} else {
usage(stderr);
return false;
}
break;
}
case 'o':
retval->output_name = strdup(optarg);
break;
case 'h':
usage(stdout);
free(retval);
return true;
case '?':
usage(stderr);
free(retval);
return false;
case 'O':
default:
if (parse_sam_global_opt(n, optarg, lopts, &retval->ga) == 0) break;
usage(stderr);
free(retval);
return false;
}
}
retval->rg_line = ks_release(&rg_line);
if (argc-optind < 1) {
fprintf(stderr, "You must specify an input file.\n");
usage(stderr);
cleanup_opts(retval);
return false;
}
if (retval->rg_id && retval->rg_line) {
fprintf(stderr, "The options -r and -R are mutually exclusive.\n");
cleanup_opts(retval);
return false;
}
if (retval->rg_line)
{
char* tmp = basic_unescape(retval->rg_line);
if ((retval->rg_id = get_rg_id(tmp)) == NULL) {
fprintf(stderr, "[%s] The supplied RG line lacks an ID tag.\n", __func__);
free(tmp);
cleanup_opts(retval);
return false;
}
retval->rg_line = tmp;
}
retval->input_name = strdup(argv[optind+0]);
*opts = retval;
return true;
}
