inline GWAS_Options get_gwas_program_options(int argc, char** argv) {
GWAS_Options result;
std::string appName = boost::filesystem::basename(argv[0]);
po::options_description optDesc("Options");
try {
/** Define and parse the program options
*/
optDesc.add_options()
("help,h", "Print help messages")
("chr,c", po::value<int>(&result.chromosome)->default_value(0), "Chromosome. Default: 0")
("in_dat,i", po::value<std::string>(&result.inputDataFile)->required(), "Input Data File")
("in_lab,l", po::value<std::string>(&result.inputLabelFile)->required(), "Input Label File")
("mappingFile,m", po::value<std::string>(&result.mappingFile)->default_value("../example/inputs/snp_mapping.csv"), "SNP-RS Mapping File. Default: ../example/inputs/snp_mapping.csv")
("in_pheno,p", po::value<std::string>(&result.inputPheno)->default_value("../example/inputs/phenotype.csv"), "Input Pheno File. Default: ../example/inputs/phenotype.csv")
("in_bayes_vertex,v", po::value<std::string>(&result.bayesVertices)->required(), "Input Bayes File")
("in_bayes_dist,d", po::value<std::string>(&result.bayesDist)->required(), "Input Dist File")
("num_perms,n", po::value<int>(&result.permutations)->default_value(1000), "Nbr Permutations. Default: 1000")
("thresholdFile,r", po::value<std::string>(&result.thresholdFile)->default_value("../example/inputs/thresholds.txt"), "Thresholds. Default: ../example/inputs/thresholds.csv")
("test,t", po::value<int>(&result.stat_test)->default_value(0), "test: 0 (chi-square)")
("sep,s", po::value<char>(&result.separator)->default_value('\t'), "Output file deliminater. Default: 'tab'")
("outDir,o", po::value<std::string>(&result.outputDir)->default_value("./out"), "Output Dir. Default: ./out")
;
po::variables_map vm;
try {
po::store(po::command_line_parser(argc, argv).options(optDesc).run(), vm); // throws on error
if (vm.count("help") ) {
samogwas::OptionPrinter::printStandardAppDesc(appName,std::cout, optDesc, NULL);
exit(1);
}
po::notify(vm);
}
catch(boost::program_options::required_option& e) /** missing arguments **/
{
samogwas::OptionPrinter::formatRequiredOptionError(e);
std::cout << e.what() << std::endl << std::endl;
samogwas::OptionPrinter::printStandardAppDesc( appName,std::cout,
optDesc, NULL);
exit(-1);
}
}
catch(std::exception e)
{
std::cout << "Unhandled Exception reached the top of main: "
<< e.what() << ", application will now exit" << std::endl;
samogwas::OptionPrinter::printStandardAppDesc(appName, std::cout, optDesc, NULL);
exit(-1);
}
return result;
}
inline GWAS_Options getGwasProgramOptions(int argc, char** argv) {
GWAS_Options result;
std::string appName = boost::filesystem::basename(argv[0]);
po::options_description optDesc("Options");
try {
/** Define and parse the program options
*/
optDesc.add_options()
("help,h", "Print help messages")
("chr,c", po::value<int>(&result.chromosome)->default_value(2), "chromosome")
("in_dat,i", po::value<std::string>(&result.inputDataFile)->required(), "Input Data File")
("in_lab,l", po::value<std::string>(&result.inputLabelFile)->required(), "Input Label File")
// ("in_imputed,i", po::value<std::string>(&result.inputDataFile)->required(), "Input Imputed Data File")
("in_pheno,p", po::value<std::string>(&result.inputPheno)->required(), "Input Pheno File")
("in_graph,g", po::value<std::string>(&result.graphFile)->required(), "Input Graph File")
("in_bayes_vertex,v", po::value<std::string>(&result.bayesVertices)->required(), "Input Bayes File")
("in_bayes_dist,d", po::value<std::string>(&result.bayesDist)->required(), "Input Dist File")
("permutations,n", po::value<int>(&result.permutations)->default_value(1000), "Nbr Permutations")
("threshold,t", po::value<double>(&result.threshold)->default_value(.005), "threshold")
("mappingFile,m", po::value<std::string>(&result.mappingFile)->required(), "SNP - RS Mapping File")
("task,k", po::value<int>(&result.task)->default_value(0), "task. 0: gwas_good_parent, 1: gwas_test")
("outDir,o", po::value<std::string>(&result.outputDir)->required(), "Output Dir")
;
po::variables_map vm;
try {
po::store(po::command_line_parser(argc, argv).options(optDesc).run(), vm); // throws on error
if (vm.count("help") ) {
samogwas::OptionPrinter::printStandardAppDesc(appName,std::cout, optDesc, NULL);
exit(1);
}
po::notify(vm);
}
catch(boost::program_options::required_option& e) /** missing arguments **/
{
samogwas::OptionPrinter::formatRequiredOptionError(e);
std::cout << e.what() << std::endl << std::endl;
samogwas::OptionPrinter::printStandardAppDesc( appName,std::cout,
optDesc, NULL);
exit(-1);
}
}
catch(std::exception e)
{
std::cout << "Unhandled Exception reached the top of main: "
<< e.what() << ", application will now exit" << std::endl;
samogwas::OptionPrinter::printStandardAppDesc(appName, std::cout, optDesc, NULL);
exit(-1);
}
return result;
}
int main( int argCount, char *argVec[] )
{
//declare *default* input file, output file, and length of radial profiles
std::string inFile;
std::string outFile;
const int radialProfileLength = 101;
//options for command line input are defined here
po::options_description optDesc("Allowed options");
optDesc.add_options()
("help","produce help message")
("in",po::value<std::string>(&inFile)->default_value("analytic.yaml"), "input file name")
("out",po::value<std::string>(&outFile)->default_value("gtcInputEq.h5"), "output file name")
;
po::variables_map varMap;
po::store(po::parse_command_line(argCount, argVec, optDesc), varMap);
po::notify(varMap);
if (varMap.count("help")) {
std::cout << optDesc << "\n";
return 1;
}
//declare YAML nodes to work with input file
YAML::Node magEq;
YAML::Node oneDim;
YAML::Node twoDim;
//declare variables to hold and manipulate intermediate data
int i; //loop index
double psi[radialProfileLength] = {0.0};
double dat[radialProfileLength] = {0.0};
//declare vars to manipulate HDF5 output file
H5::H5File outfile( outFile, H5F_ACC_TRUNC );
hsize_t dim[1] = { (unsigned int)radialProfileLength };
H5::DataSpace datspace1D( 1, dim );
H5::IntType dattype( H5::PredType::NATIVE_DOUBLE );
H5::DataSet datset;
//read in the YAML eq file
magEq = YAML::LoadFile( inFile );
//generate radial coords
for ( i=0; i<radialProfileLength; i++ )
psi[i] = i/(radialProfileLength - 1.0);
//do some parsing
//first check for 1D and 2D data in the eq file
//if the exist, generate profiles from polynomial coefficients
if(magEq["1D profiles"]){
oneDim = magEq["1D profiles"];
for(YAML::const_iterator iter=oneDim.begin(); iter!=oneDim.end(); ++iter){
for( i=0; i<radialProfileLength; i++)
dat[i] = iter->second[0].as<double>()
+ iter->second[1].as<double>()*psi[i]
+ iter->second[2].as<double>()*psi[i]*psi[i];
datset = outfile.createDataSet( iter->first.as<std::string>(), dattype, datspace1D );
datset.write( dat, H5::PredType::NATIVE_DOUBLE );
}
}
if(magEq["2d profiles"]){
twoDim = magEq["2D profiles"];
// do some more parsing if we need this part...
}
return 0;
}
int
main(int argc, char* argv[])
{
Options options;
options.freshnessPeriod = getMinimumFreshnessPeriod();
options.shouldLimitSatisfied = false;
options.nMaxPings = 0;
options.shouldPrintTimestamp = false;
options.payloadSize = 0;
namespace po = boost::program_options;
po::options_description visibleOptDesc("Allowed options");
visibleOptDesc.add_options()
("help,h", "print this message and exit")
("version,V", "display version and exit")
("freshness,x", po::value<int>(),
("set freshness period in milliseconds (minimum " +
std::to_string(getMinimumFreshnessPeriod().count()) + " ms)").c_str())
("satisfy,p", po::value<int>(&options.nMaxPings), "set maximum number of pings to be satisfied")
("timestamp,t", "log timestamp with responses")
("size,s", po::value<int>(&options.payloadSize), "specify size of response payload")
;
po::options_description hiddenOptDesc("Hidden options");
hiddenOptDesc.add_options()
("prefix", po::value<std::string>(), "prefix to register")
;
po::options_description optDesc("Allowed options");
optDesc.add(visibleOptDesc).add(hiddenOptDesc);
try {
po::positional_options_description optPos;
optPos.add("prefix", -1);
po::variables_map optVm;
po::store(po::command_line_parser(argc, argv).options(optDesc).positional(optPos).run(), optVm);
po::notify(optVm);
if (optVm.count("help") > 0) {
usage(visibleOptDesc);
}
if (optVm.count("version") > 0) {
std::cout << "ndnpingserver " << tools::VERSION << std::endl;
exit(0);
}
if (optVm.count("prefix") > 0) {
options.prefix = Name(optVm["prefix"].as<std::string>());
}
else {
std::cerr << "ERROR: No prefix specified" << std::endl;
usage(visibleOptDesc);
}
if (optVm.count("freshness") > 0) {
options.freshnessPeriod = time::milliseconds(optVm["freshness"].as<int>());
if (options.freshnessPeriod.count() < getMinimumFreshnessPeriod().count()) {
std::cerr << "ERROR: Specified FreshnessPeriod is less than the minimum "
<< getMinimumFreshnessPeriod() << std::endl;
usage(visibleOptDesc);
}
}
if (optVm.count("satisfy") > 0) {
options.shouldLimitSatisfied = true;
if (options.nMaxPings < 1) {
std::cerr << "ERROR: Maximum number of pings to satisfy must be greater than 0" << std::endl;
usage(visibleOptDesc);
}
}
if (optVm.count("timestamp") > 0) {
options.shouldPrintTimestamp = true;
}
if (optVm.count("size") > 0) {
if (options.payloadSize < 0) {
std::cerr << "ERROR: Payload size must be greater than or equal to 0" << std::endl;
usage(visibleOptDesc);
}
}
}
catch (const po::error& e) {
std::cerr << "ERROR: " << e.what() << std::endl;
usage(visibleOptDesc);
}
std::cout << "PING SERVER " << options.prefix << std::endl;
return Runner(options).run();
}
