int vcf_tool_merge(int argc, char *argv[], const char *configuration_file, array_list_t *config_search_paths) {
/* ******************************
* Modifiable options *
* ******************************/
shared_options_t *shared_options = new_shared_cli_options(0);
merge_options_t *merge_options = new_merge_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_merge_options(merge_options, shared_options, arg_end(NUM_MERGE_OPTIONS));
show_usage("hpg-var-vcf merge", argtable);
arg_freetable(argtable, NUM_MERGE_OPTIONS);
return 0;
}
/* ******************************
* Execution steps *
* ******************************/
// Step 1: read options from configuration file
int config_errors = read_shared_configuration(configuration_file, shared_options);
config_errors &= read_merge_configuration(configuration_file, merge_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
// If no arguments or only --help are provided, show usage
argtable = parse_merge_options(argc, argv, merge_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_merge_options(merge_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);
merge_options_data_t *options_data = new_merge_options_data(merge_options, config_search_paths);
init_log_custom(shared_options_data->log_level, 1, "hpg-var-vcf.log", "w");
// Step 5: Perform the requested task
int result = run_merge(shared_options_data, options_data);
free_merge_options_data(options_data);
free_shared_options_data(shared_options_data);
arg_freetable(argtable, NUM_MERGE_OPTIONS);
return 0;
}
int vcf_tool_split(int argc, char *argv[], const char *configuration_file) {
/* ******************************
* Modifiable options *
* ******************************/
shared_options_t *shared_options = new_shared_cli_options();
split_options_t *split_options = new_split_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_split_options(split_options, shared_options, arg_end(split_options->num_options + shared_options->num_options));
show_usage("hpg-var-vcf split", argtable, split_options->num_options + shared_options->num_options);
arg_freetable(argtable, split_options->num_options + shared_options->num_options - 11);
return 0;
}
/* ******************************
* Execution steps *
* ******************************/
// Step 1: read options from configuration file
int config_errors = read_shared_configuration(configuration_file, shared_options);
config_errors &= read_split_configuration(configuration_file, split_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_split_options(argc, argv, split_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_split_options(split_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);
split_options_data_t *options_data = new_split_options_data(split_options);
// Step 5: Perform the requested task
int result = run_split(shared_options_data, options_data);
free_split_options_data(options_data);
free_shared_options_data(shared_options_data);
arg_freetable(argtable, split_options->num_options + shared_options->num_options - 11);
return 0;
}
int association(int argc, char *argv[], const char *configuration_file) {
/* ******************************
* Modifiable options *
* ******************************/
shared_options_t *shared_options = new_shared_cli_options();
assoc_options_t *assoc_options = new_assoc_cli_options();
// If no arguments or only --help are provided, show usage
void **argtable;
if (argc == 1 || !strcmp(argv[1], "--help")) {
argtable = merge_assoc_options(assoc_options, shared_options, arg_end(assoc_options->num_options + shared_options->num_options));
show_usage("hpg-var-gwas assoc", argtable, assoc_options->num_options + shared_options->num_options);
arg_freetable(argtable, assoc_options->num_options + shared_options->num_options);
return 0;
}
/* ******************************
* Execution steps *
* ******************************/
// Step 1: read options from configuration file
int config_errors = read_shared_configuration(configuration_file, shared_options);
config_errors &= read_assoc_configuration(configuration_file, assoc_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_assoc_options(argc, argv, assoc_options, shared_options);
// Step 3: check that all options are set with valid values
// Mandatory options that couldn't be read from the config file must be set via command-line
// If not, return error code!
int check_assoc_opts = verify_assoc_options(assoc_options, shared_options);
if (check_assoc_opts > 0) {
return check_assoc_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);
assoc_options_data_t *options_data = new_assoc_options_data(assoc_options);
// Step 5: Perform the operations related to the selected GWAS sub-tool
// switch (options_data->task) {
// case TDT:
// run_tdt_test(shared_options_data, options_data);
// break;
// case ASSOCIATION_BASIC:
// case FISHER:
run_association_test(shared_options_data, options_data);
// break;
// }
free_assoc_options_data(options_data);
free_shared_options_data(shared_options_data);
arg_freetable(argtable, assoc_options->num_options + shared_options->num_options);
return 0;
}
