Settings::Settings(int argc, char** args)
{
// parse program arguments
if (argc < 4) {
if (argc == 1) {
printProgramInfo();
} else {
std::string arg = args[1];
if (arg == "-h" || arg == "--help") {
printUsage();
exit(EXIT_SUCCESS);
} else if (arg == "-i" || arg == "--info") {
printProgramInfo();
exit(EXIT_SUCCESS);
}
}
printUsage();
exit(EXIT_FAILURE);
}
//set standard values
num_threads_ = std::thread::hardware_concurrency();
essa_k_ = 1;
max_passes_ = 2;
min_len_ = 20;
directory_ = "Jabba_output";
output_mode_ = SHORT;
std::string graph_name = "DBGraph.fasta";
FileType file_type(FASTA);
std::vector<std::string> libraries;
// extract the other parameters
for (int i = 1; i < argc; i++) {
std::string arg(args[i]);
if (arg.empty()) continue;// this shouldn't happen
if (arg == "-fastq") { // file type
std::cout << "FileType is fastq." << std::endl;
file_type = FASTQ;
} else if (arg == "-fasta") {
std::cout << "FileType is fasta." << std::endl;
file_type = FASTA;
} else if (arg == "-t" || arg == "--threads") {
++i;
num_threads_ = std::stoi(args[i]);
} else if (arg == "-g" || arg == "--graph") {
++i;
graph_name = args[i];
} else if (arg == "-k" || arg == "--dbgk") {
++i;
dbg_k_ = std::stoi(args[i]);
} else if (arg == "-e" || arg == "--essak") {
++i;
essa_k_ = std::stoi(args[i]);
} else if (arg == "-p" || arg == "--passes") {
++i;
max_passes_ = std::stoi(args[i]);
} else if (arg == "-l" || arg == "--length") {
++i;
min_len_ = std::stoi(args[i]);
} else if (arg == "-o" || arg == "--output") {
++i;
directory_ = args[i];
} else if (arg == "-s" || arg == "--short") {
std::cerr << "-s --short is deprecated, short is now the default output mode.\n";
output_mode_ = SHORT;
} else if (arg == "-m" || arg == "--outputmode") {
++i;
if (std::string(args[i]) == std::string("short")) {
output_mode_ = SHORT;
} else if (std::string(args[i]) == std::string("long")) {
output_mode_ = LONG;
} else {
std::cerr << args[i] << " is not a valid output mode. Use \"long\" or \"short\" instead.\n";
}
} else {// filename
libraries.push_back(args[i]);
}
}
for (auto const &lib : libraries) {
libraries_.insert(ReadLibrary(lib, directory_));
}
//
graph_ = new ReadLibrary(graph_name, "");
// try to create the output directory
#ifdef _MSC_VER
CreateDirectory(directory_.c_str(), NULL);
#else
DIR * dir = opendir(directory_.c_str());
if ((dir == NULL) && (mkdir(directory_.c_str(), 0777) != 0))
throw std::ios_base::failure("Can't create directory: " + directory_);
closedir(dir);
#endif
// log the instructions
logInstructions(argc, args);
//print settings
std::cout << "Max Number of Threads is " << num_threads_ << std::endl;
std::cout << "Graph is " << graph_->getInputFilename() << std::endl;
std::cout << "DBG K is " << dbg_k_ << std::endl;
std::cout << "ESSA K is " << essa_k_ << std::endl;
std::cout << "Max Passes is " << max_passes_ << std::endl;
std::cout << "Min Seed Size is " << min_len_ << std::endl;
std::cout << "Output Directory is " << directory_ << std::endl;
std::cout << "Output Mode is ";
if (output_mode_ == SHORT){
std::cout << "short" << std::endl;
} else if (output_mode_ == LONG){
std::cout << "long" << std::endl;
} else {
std::cout << "not implemented" << std::endl;
}
}
bool DefFile::Read()
{
stream = new std::fstream(fileName.c_str(), std::ios::in);
if (stream != NULL)
{
try
{
lineno = 0;
NextToken();
while (!stream->eof())
{
if (token->IsEnd())
{
NextToken();
}
else if (!token->IsKeyword())
{
throw new std::runtime_error("Invalid directive");
}
else
{
switch(token->GetKeyword())
{
case edt_name:
ReadName();
break;
case edt_library:
ReadLibrary();
break;
case edt_exports:
ReadExports();
break;
case edt_imports:
ReadImports();
break;
case edt_description:
ReadDescription();
break;
case edt_stacksize:
ReadStacksize();
break;
case edt_heapsize:
ReadHeapsize();
break;
case edt_code:
ReadCode();
break;
case edt_data:
ReadData();
break;
case edt_sections:
ReadSections();
break;
default:
throw new std::runtime_error("Invalid directive");
}
}
}
}
catch (std::runtime_error *e)
{
std::cout << fileName << "(" << lineno << "): " << e->what() << std::endl ;
delete e;
}
delete stream;
}
else
{
std::cout << "File '" << name << "' not found." << std::endl;
}
return true;
}