static void get_options(int argc, char **argv, const char *progname)
{
signed char c;
char tmp[512];
char *catalog_host = NULL;
int catalog_port = 0;
while((c = getopt(argc, argv, "p:P:n:d:F:N:C:s:r:R:k:w:c:o:uxvhaZ:")) > -1) {
switch (c) {
case 'p':
port = atoi(optarg);
break;
case 'r':
repeat_filename = optarg;
break;
case 'R':
retry_max = atoi(optarg);
break;
case 's':
rectangle_size = atoi(optarg);
break;
case 'k':
kmer_size = atoi(optarg);
break;
case 'w':
window_size = atoi(optarg);
break;
case 'c':
checkpoint_filename = optarg;
break;
case 'd':
debug_flags_set(optarg);
break;
case 'F':
wq_option_fast_abort_multiplier = atof(optarg);
break;
case 'a':
work_queue_master_mode = WORK_QUEUE_MASTER_MODE_CATALOG;
break;
case 'N':
free(project);
project = xxstrdup(optarg);
break;
case 'P':
priority = atoi(optarg);
break;
case 'C':
if(!parse_catalog_server_description(optarg, &catalog_host, &catalog_port)) {
fprintf(stderr, "sand_filter: catalog server should be given as HOSTNAME:PORT'.\n");
exit(1);
}
setenv("CATALOG_HOST", catalog_host, 1);
char *value = string_format("%d", catalog_port);
setenv("CATALOG_PORT", value, 1);
free(value);
work_queue_master_mode = WORK_QUEUE_MASTER_MODE_CATALOG;
break;
case 'u':
do_not_unlink = 1;
break;
case 'Z':
port_file = optarg;
port = 0;
break;
case 'o':
debug_config_file(optarg);
break;
case 'v':
cctools_version_print(stdout, progname);
exit(0);
default:
case 'h':
show_help(progname);
exit(0);
}
}
cctools_version_debug(D_DEBUG, argv[0]);
if(argc - optind != 2) {
show_help(progname);
exit(1);
}
sequence_filename = argv[optind++];
outfilename = argv[optind++];
outdirname = malloc(strlen(outfilename) + 15);
sprintf(outdirname, "%s.filter.tmp", outfilename);
if(mkdir(outdirname, S_IRWXU) != 0) {
if(errno == EEXIST) {
fprintf(stderr, "%s: directory %s already exists, you may want to delete or rename before running.\n", progname, outdirname);
} else {
fprintf(stderr, "%s: couldn't create %s: %s\n", progname, outdirname, strerror(errno));
exit(1);
}
}
sprintf(filter_program_args, "-k %d -w %d -s d", kmer_size, window_size);
if(repeat_filename) {
sprintf(tmp, " -r %s", string_basename(repeat_filename));
strcat(filter_program_args, tmp);
}
}
static void work_queue_status_parse_command_line_arguments(int argc, char *argv[])
{
signed int c;
static struct option long_options[] = {
{"statistics", no_argument, 0, 'Q'},
{"workers", no_argument, 0, 'W'},
{"tasks", no_argument, 0, 'T'},
{"verbose", no_argument, 0, 'l'},
{"resources", no_argument, 0, 'R'},
{"catalog", required_argument, 0, 'C'},
{"debug", required_argument, 0, 'd'},
{"timeout", required_argument, 0, 't'},
{"help", no_argument, 0, 'h'},
{0,0,0,0}};
while((c = getopt_long(argc, argv, "QTWC:d:lo:O:Rt:vh", long_options, NULL)) > -1) {
switch (c) {
case 'C':
if(!parse_catalog_server_description(optarg, &catalog_host, &catalog_port)) {
fprintf(stderr, "Cannot parse catalog description: %s. \n", optarg);
exit(EXIT_FAILURE);
}
break;
case 'd':
debug_flags_set(optarg);
break;
case 'Q':
query_mode = QUERY_QUEUE;
break;
case 'T':
query_mode = QUERY_TASKS;
break;
case 'W':
query_mode = QUERY_WORKERS;
break;
case 'l':
format_mode = FORMAT_LONG;
break;
case 'o':
debug_config_file(optarg);
break;
case 'O':
debug_config_file_size(string_metric_parse(optarg));
break;
case 't':
work_queue_status_timeout = strtol(optarg, NULL, 10);
break;
case 'h':
show_help(argv[0]);
exit(EXIT_SUCCESS);
break;
case 'R':
query_mode = QUERY_MASTER_RESOURCES;
resource_mode = 1;
break;
case 'v':
cctools_version_print(stdout, argv[0]);
exit(EXIT_SUCCESS);
default:
show_help(argv[0]);
exit(EXIT_FAILURE);
break;
}
}
}
