コード例 #1
0
ファイル: bam_addrprg.c プロジェクト: BIGLabHYU/samtools
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;
}
コード例 #2
0
ファイル: bam_split.c.pysam.c プロジェクト: jwhsanger/pysam
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;
}
コード例 #3
0
ファイル: bam_addrprg.c プロジェクト: BIGLabHYU/samtools
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;
}