int
main (int argc, char **argv)
{
struct gengetopt_args_info args_info;
/* let's call our cmdline parser */
if (my_cmdline_parser (argc, argv, &args_info) != 0)
exit(1) ;
if (args_info.help_given)
{
printf ("This is a simple test for gengetopt\n");
my_cmdline_parser_print_help ();
}
if (args_info.full_help_given)
{
printf ("This is a simple test for gengetopt\n");
my_cmdline_parser_print_full_help ();
}
if (args_info.version_given)
{
printf ("Here is the version\n");
my_cmdline_parser_print_version ();
}
return 0;
}
int main(int argc, char * argv[])
{
int isExitWithHelp = 0;
alder_gc_option_t option;
struct gengetopt_args_info args_info;
if (my_cmdline_parser (argc, argv, &args_info) != 0) exit(1) ;
isExitWithHelp = alder_gc_option_init(&option, &args_info);
if (isExitWithHelp == 1) {
my_cmdline_parser_free(&args_info);
alder_gc_option_free(&option);
exit(1);
}
if (args_info.dpgc_given) {
main_dpgb();
}
if (args_info.bdwgc_given) {
alder_bdwgc();
}
my_cmdline_parser_free(&args_info);
alder_gc_option_free(&option);
return 0;
}
int main(int argc, char * argv[])
{
int isExitWithHelp = 0;
alder_mcas_option_t option;
struct gengetopt_args_info args_info;
if (my_cmdline_parser (argc, argv, &args_info) != 0) exit(1) ;
isExitWithHelp = alder_mcas_option_init(&option, &args_info);
if (isExitWithHelp == 1) {
my_cmdline_parser_free(&args_info);
alder_mcas_option_free(&option);
exit(1);
}
my_cmdline_parser_free(&args_info);
alder_mcas_option_free(&option);
return 0;
}
int main(int argc, char * argv[])
{
///////////////////////////////////////////////////////////////////////////
// Check the command line arguments.
alder_file_option_t option;
struct gengetopt_args_info args_info;
if (my_cmdline_parser (argc, argv, &args_info) != 0) exit(1) ;
int isExitWithHelp = alder_file_option_init(&option, &args_info);
if (isExitWithHelp == 1) {
alder_file_option_free(&option);
my_cmdline_parser_free(&args_info);
exit(1);
}
if (args_info.summary_flag) {
for (size_t i = 0; i < args_info.inputs_num; i++) {
alder_file(args_info.inputs[i]);
}
}
if (args_info.numline_flag) {
fprintf(option.fout, "--- Number of Lines in the Files ---\n");
for (size_t i = 0; i < args_info.inputs_num; i++) {
if (alder_file_isfile(args_info.inputs[i]) &&
!alder_file_isbinary(args_info.inputs[i])) {
int64_t n = alder_file_numline(args_info.inputs[i]);
fprintf(option.fout, "%s: %lld\n", args_info.inputs[i], n);
}
}
}
if (args_info.disk_flag) {
for (size_t i = 0; i < args_info.inputs_num; i++) {
unsigned long space_mb = 0;
int s = alder_file_availablediskspace(args_info.inputs[i], &space_mb);
if (s == 0) {
fprintf(option.fout, "Available space in %s: %lu MB\n",
args_info.inputs[i], space_mb);
}
}
}
if (args_info.estimate_sequence_file_flag) {
for (size_t i = 0; i < args_info.inputs_num; i++) {
unsigned long space_mb = 0;
int s = alder_file_sequencefilesize(args_info.inputs[i], &space_mb);
if (s == 0) {
fprintf(option.fout, "Estimated sequence size in %s: %lu MB\n",
args_info.inputs[i], space_mb);
} else {
fprintf(option.fout, "File %s is not a proper file.\n",
args_info.inputs[i]);
}
}
}
if (args_info.mkdir_given) {
alder_file_mkdir(args_info.mkdir_arg);
}
if (args_info.cpu_flag) {
int ncpu = alder_file_sysctl();
fprintf(stdout, "Number of CPU: %d\n", ncpu);
}
if (args_info.memory_flag) {
alder_file_memory_test();
}
if (args_info.io_flag) {
alder_file_io_test03(args_info.inputs[0]);
// alder_file_io_test01();
// alder_file_io_test();
}
if (args_info.stdin_flag) {
alder_file_io_stdin();
}
if (args_info.stdout_flag) {
alder_file_io_stdout();
}
alder_file_option_free(&option);
my_cmdline_parser_free(&args_info);
return 0;
}
/**
* This function is the main function where commands are called via
* other functions in the kmer library.
*
* @param argc argc
* @param argv argv
*
* @return program exit value (0 on SUCCESS, otherwise other values)
*/
int main(int argc, char * argv[])
{
time_t start = time(NULL);
int s = ALDER_STATUS_SUCCESS;
int isExitWithHelp = 0;
alder_kmer_option_t option;
struct gengetopt_args_info args_info;
if (my_cmdline_parser (argc, argv, &args_info) != 0) exit(1) ;
isExitWithHelp = alder_kmer_option_init(&option, &args_info, argc);
if (isExitWithHelp != 0) {
my_cmdline_parser_free(&args_info);
alder_kmer_option_free(&option);
exit(isExitWithHelp);
}
///////////////////////////////////////////////////////////////////////////
// Set up a log file if needed.
alder_file_rm(args_info.log_arg);
if (args_info.log_given) {
alder_logger_initialize(args_info.log_arg, (int)args_info.loglevel_arg);
alder_logger_error_initialize(LOG_WARNING);
} else {
alder_logger_initialize(args_info.log_arg, LOG_SILENT);
alder_logger_error_initialize(LOG_BASIC);
}
///////////////////////////////////////////////////////////////////////////
// Timing:
alder_log("START: %.*s", (int)(strlen(ctime(&start))-1), ctime(&start));
///////////////////////////////////////////////////////////////////////////
// Count:
if (args_info.count_flag) {
PlantSeeds(args_info.seed_arg);
SelectStream(1);
command_count_t count;
if (args_info.dsk_flag == 0) {
count = &alder_kmer_topkmer;
args_info.only_init_flag = (int)option.format;
args_info.no_count_flag = args_info.save_all_flag;
} else {
count = &alder_kmer_count;
args_info.select_version_arg = 7;
}
s = (*count)(args_info.select_version_arg,
(int)args_info.kmer_arg,
args_info.totalmaxkmer_arg,
args_info.disk_arg,
args_info.memory_arg,
(int)args_info.lower_count_arg,
(int)args_info.upper_count_arg,
option.maxfile,
args_info.inbuffer_arg,
args_info.outbuffer_arg,
(int)args_info.ni_arg,
(int)args_info.np_arg,
(int)args_info.nh_arg,
(int)args_info.nthread_arg,
args_info.progress_flag,
args_info.progress_to_stderr_flag,
args_info.only_init_flag,
args_info.no_delete_flag,
args_info.no_partition_flag,
args_info.no_count_flag,
option.infile,
args_info.outfile_given,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// Partition:
if (args_info.partition_flag) {
s = alder_kmer_partition(args_info.select_version_arg,
(int)args_info.kmer_arg,
args_info.disk_arg,
args_info.memory_arg,
args_info.min_table_memory_arg,
args_info.max_table_memory_arg,
option.maxfile,
args_info.inbuffer_arg,
args_info.outbuffer_arg,
(int)args_info.ni_arg,
(int)args_info.np_arg,
(int)args_info.nh_arg,
(int)args_info.nthread_arg,
args_info.progress_flag,
args_info.progress_to_stderr_flag,
args_info.use_seqfile_flag,
args_info.binfile_arg,
args_info.binfile_given,
option.infile,
args_info.outfile_given,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// Table:
if (args_info.table_flag) {
s = alder_kmer_table(args_info.select_version_arg,
0, // -1, why -1?
(int)args_info.kmer_arg,
// args_info.disk_arg,
args_info.memory_arg,
option.maxfile,
args_info.inbuffer_arg,
args_info.outbuffer_arg,
(int)args_info.ni_arg,
(int)args_info.np_arg,
(int)args_info.nh_arg,
(int)args_info.nthread_arg,
args_info.progress_flag,
args_info.progress_to_stderr_flag,
(int)args_info.lower_count_arg,
(int)args_info.upper_count_arg,
args_info.parfile_arg,
args_info.parfile_given,
option.infile,
args_info.outfile_given,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// Report/Dump:
if (args_info.report_flag) {
if (args_info.dsk_flag == 1) {
args_info.select_version_arg = 7;
}
if (args_info.query_given) {
s = alder_kmer_report(args_info.select_version_arg,
bdata(option.infile->entry[0]),
args_info.summary_flag,
args_info.sequence_arg);
} else {
s = alder_kmer_report(args_info.select_version_arg,
bdata(option.infile->entry[0]),
args_info.summary_flag,
NULL);
}
}
///////////////////////////////////////////////////////////////////////////
// Query:
if (args_info.query_flag) {
s = alder_kmer_query(args_info.select_version_arg,
bdata(option.infile->entry[0]),
args_info.summary_flag,
args_info.sequence_arg);
}
///////////////////////////////////////////////////////////////////////////
// Simulation:
if (args_info.simulate_flag) {
PlantSeeds(args_info.seed_arg);
SelectStream(1);
if (args_info.error_rate_arg > 0) {
s = alder_kmer_simulate2(args_info.select_version_arg,
args_info.outfile_given,
args_info.outfile_arg,
args_info.outdir_arg,
option.format,
(int)args_info.nf_arg,
args_info.seed_arg,
(int)args_info.error_rate_arg,
(int)args_info.error_initial_arg,
(int)args_info.error_iteration_arg,
(int)args_info.error_duplicate_arg,
(int)args_info.kmer_arg,
(int)args_info.seqlen_arg,
(size_t)args_info.maxkmer_arg,
args_info.progress_flag,
args_info.progress_to_stderr_flag);
} else {
s = alder_kmer_simulate(args_info.select_version_arg,
args_info.outfile_given,
args_info.outfile_arg,
args_info.outdir_arg,
option.format,
args_info.with_parfile_flag,
(int)args_info.nf_arg,
(int)args_info.ni_arg,
(int)args_info.np_arg,
(int)args_info.kmer_arg,
(int)args_info.seqlen_arg,
(size_t)args_info.maxkmer_arg,
args_info.progress_flag,
args_info.progress_to_stderr_flag);
}
}
///////////////////////////////////////////////////////////////////////////
// Decode/Kmer:
if (args_info.decode_flag) {
s = alder_kmer_decode((int)args_info.kmer_arg,
args_info.progress_flag,
option.infile,
args_info.outfile_given,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// List:
if (args_info.list_flag) {
s = alder_kmer_list((int)args_info.kmer_arg,
args_info.with_index_flag,
option.infile,
args_info.outfile_given,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// Match:
if (args_info.match_flag) {
s = alder_kmer_match(args_info.progress_flag,
option.infile,
args_info.tabfile_arg,
args_info.format_arg,
args_info.outfile_given,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// Uncompress:
if (args_info.uncompress_flag) {
alder_kmer_uncompress(args_info.progress_flag,
option.infile,
args_info.outfile_given,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// View:
if (args_info.view_flag) {
alder_kmer_view((int)args_info.format_arg,
option.infile,
args_info.outfile_given,
args_info.outdir_arg,
args_info.outfile_arg,
(int)args_info.kmer_arg);
}
///////////////////////////////////////////////////////////////////////////
// Binary:
if (args_info.binary_flag) {
size_t n_byte = 0;
uint64_t n_kmer = 0;
uint64_t n_dna = 0;
uint64_t n_seq = 0;
size_t n_totalfilesize = 0;
size_t subsize = ALDER_KMER_BUFSIZE;
s = alder_kmer_binary(NULL, 0, subsize,
&n_kmer, &n_dna, &n_seq,
&n_totalfilesize,
&n_byte,
args_info.select_version_arg,
(int)args_info.kmer_arg,
args_info.disk_arg,
args_info.memory_arg,
args_info.min_table_memory_arg,
args_info.max_table_memory_arg,
(int)args_info.nsplit_arg,
args_info.progress_flag,
args_info.progress_to_stderr_flag,
option.infile,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// Assess:
if (args_info.assess_flag) {
alder_kmer_assess((int)args_info.upper_count_arg,
args_info.tabfile_arg,
option.infile,
(int)args_info.outfile_given,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// Inspect:
if (args_info.inspect_flag) {
alder_kmer_inspect(option.infile,
args_info.outdir_arg,
args_info.outfile_arg);
}
///////////////////////////////////////////////////////////////////////////
// Timing:
time_t end = time(NULL);
alder_log("END: %.*s", (int)(strlen(ctime(&end))-1), ctime(&end));
double run_time = difftime(end, start);
alder_log("RUN TIME: %.f (s) = %.f (m) = %.f (h)", run_time, run_time/60, run_time/3600);
///////////////////////////////////////////////////////////////////////////
// Cleanup!
alder_logger_finalize();
alder_logger_error_finalize();
if (!args_info.log_given) {
alder_file_rm(args_info.log_arg);
}
my_cmdline_parser_free(&args_info);
alder_kmer_option_free(&option);
return s;
}
