int vcf_tool_stats(int argc, char *argv[], const char *configuration_file) {
/* ******************************
* Modifiable options *
* ******************************/
shared_options_t *shared_options = new_shared_cli_options();
stats_options_t *stats_options = new_stats_cli_options();
// If no arguments or only --help are provided, show usage
void **argtable;
if (argc == 1 || !strcmp(argv[1], "-h") || !strcmp(argv[1], "--help")) {
argtable = merge_stats_options(stats_options, shared_options, arg_end(stats_options->num_options + shared_options->num_options));
show_usage("hpg-var-vcf stats", argtable, stats_options->num_options + shared_options->num_options);
arg_freetable(argtable, stats_options->num_options + shared_options->num_options - 10);
return 0;
}
/* ******************************
* Execution steps *
* ******************************/
// Step 1: read options from configuration file
int config_errors = read_shared_configuration(configuration_file, shared_options);
config_errors &= read_stats_configuration(configuration_file, stats_options, shared_options);
if (config_errors) {
LOG_FATAL("Configuration file read with errors\n");
return CANT_READ_CONFIG_FILE;
}
// Step 2: parse command-line options
argtable = parse_stats_options(argc, argv, stats_options, shared_options);
// Step 3: check that all options are set with valid values
// Mandatory that couldn't be read from the config file must be set via command-line
// If not, return error code!
int check_vcf_tools_opts = verify_stats_options(stats_options, shared_options);
if (check_vcf_tools_opts > 0) {
return check_vcf_tools_opts;
}
// Step 4: Create XXX_options_data_t structures from valid XXX_options_t
shared_options_data_t *shared_options_data = new_shared_options_data(shared_options);
stats_options_data_t *options_data = new_stats_options_data(stats_options);
// Step 5: Perform the requested task
int result = run_stats(shared_options_data, options_data);
free_stats_options_data(options_data);
free_shared_options_data(shared_options_data);
arg_freetable(argtable, stats_options->num_options + shared_options->num_options - 10);
return 0;
}
const saladstate_t parse_options(int argc, char* argv[], config_t* const config, test_config_t* const test_config)
{
assert(argv != NULL);
assert(config != NULL);
assert(test_config != NULL);
if (argc <= 1)
{
return SALAD_HELP;
}
*config = DEFAULT_CONFIG;
*test_config = DEFAULT_TEST_CONFIG;
if (*argv[1] != '-')
{
config->mode = to_saladmode(argv[1]);
switch (config->mode)
{
case TRAINING: return parse_training_options(argc, argv, config);
case PREDICT: return parse_predict_options(argc, argv, config);
case INSPECT: return parse_inspect_options(argc, argv, config);
case STATS: return parse_stats_options(argc, argv, config);
#ifdef TEST_SALAD
case TEST: return parse_test_options(argc, argv, test_config);
#endif
default:
error("Unknown mode '%s'.", argv[1]);
return SALAD_EXIT;
}
}
int option;
while ((option = getopt_long(argc, argv, MAIN_OPTION_STR, main_longopts, NULL)) != -1)
{
switch (option)
{
case '?':
case 'h':
return SALAD_HELP;
case 'v':
return SALAD_VERSION;
default: break;
}
}
return SALAD_EXIT;
}
