int main(int argc, char *argv[]){
if(argc <= 1){
printProgramInfo();
return 0;
}
initData();
dataIndex = 0;
pSourceCodeFile = fopen(argv[1], "rb");
int cmd = 0;
if (pSourceCodeFile==NULL){
fatalError(FILE_OPEN_FAILED_ERROR_MSG);
}
while(!feof(pSourceCodeFile)){
cmd = getNextCommand();
if(cmd!=EOF){
execCommand(cmd);
}
}
fclose(pSourceCodeFile);
msg(EXECUTION_FINISHED_MSG);
return 0;
}
void OpenCLPrinter::printKernelInfo(cl::Kernel kernel)
{
print("--- KernelInfo ---", "");
cl::STRING_CLASS functionName = kernel.getInfo<CL_KERNEL_FUNCTION_NAME>();
cl::Context context = kernel.getInfo<CL_KERNEL_CONTEXT>();
cl::Program program = kernel.getInfo<CL_KERNEL_PROGRAM>();
print("Function name", functionName);
printContextInfo(context);
printProgramInfo(program);
}
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;
}
}
