void Command::btUsage(){
fprintf(stderr, "Usage: shrek binary [options] \n\n");
fprintf(stderr, "Required Arguments:\n");
fprintf(stderr, " -p | --pfile P-value file name\n");
fprintf(stderr, " -r | --bfile Reference Panel file prefix\n"); //Currently we only support plink format
fprintf(stderr, " -K | --prevalence Population Prevalence of the trait\n");
fprintf(stderr, " -s | --stat Column name for summary statistic / p-value\n");
fprintf(stderr, " -S | --sign Column name for direction of effect\n");
fprintf(stderr, " e.g. OR, Z e.t.c\n");
fprintf(stderr, " -U | --null Null for direction of effect [0]\n");
fprintf(stderr, " e.g. -U 1 for OR, 0 for others\n");
fprintf(stderr, " -v | --conIndex Column containing the number of controls\n");
fprintf(stderr, " -V | --nControl Number of controls\n");
fprintf(stderr, " Only functional when -v not provided\n");
fprintf(stderr, " -w | --caseIndex Column containing the number of cases\n");
fprintf(stderr, " -W | --nCase Number of cases\n");
fprintf(stderr, " Only functional when -w not provided\n");
fprintf(stderr, " -c | --chr Column name for chromosome \n");
fprintf(stderr, " -m | --rs Column name for rsID \n");
fprintf(stderr, " -l | --loc Column name for coordinate \n");
fprintf(stderr, " -a | --ref Column name for reference allele\n");
fprintf(stderr, " -A | --alt Column name for alternative allele\n");
fprintf(stderr, " -i | --info Column name for impute info score\n");
generalOptions();
}
void MainWindow::writeConfig(KSharedConfigPtr config)
{
KConfigGroup generalOptions(config, "General Options");
m_recentFiles->saveEntries(KConfigGroup(config, "Recent Files"));
config->sync();
}
void Command::qtUsage(){
fprintf(stderr, "Usage: shrek quant [options] \n\n");
fprintf(stderr, "Required Arguments:\n");
fprintf(stderr, " -p | --pfile P-value file name\n");
fprintf(stderr, " -r | --bFile Reference Panel file prefix\n"); //Currently we only support plink format
fprintf(stderr, " -x | --extreme Extreme Adjustment, can be calculated as: \n");
fprintf(stderr, " Variance before selection / Variance after selection\n");
fprintf(stderr, " -n | --sampIndex Column name for the number of sample\n");
fprintf(stderr, " -N | --nSample Number of sample in the study\n");
fprintf(stderr, " Only functional when -n not provided\n");
fprintf(stderr, " -s | --stat Column name for summary statistic / p-value\n");
fprintf(stderr, " -S | --sign Column name for direction of effect\n");
fprintf(stderr, " e.g. OR, Z e.t.c\n");
fprintf(stderr, " -U | --null Null for direction of effect [0]\n");
fprintf(stderr, " e.g. -U 1 for OR, 0 for others\n");
fprintf(stderr, " -c | --chr Column name for chromosome \n");
fprintf(stderr, " -m | --rs Column name for rsID \n");
fprintf(stderr, " -l | --loc Column name for coordinate \n");
fprintf(stderr, " -A | --ref Column name for reference allele\n");
fprintf(stderr, " -a | --alt Column name for alternative allele\n");
fprintf(stderr, " -i | --info Column name for impute info score\n");
generalOptions();
}
bool IV::init( const int ac, char ** av )
{
if( _init )
return true;
_init = true;
Global& global = Global::getInstance();
boost::program_options::options_description cmdOptions;
// General Options
boost::program_options::options_description generalOptions("General options");
generalOptions.add_options()
("help", "produce help message");
// Behavior Options
boost::program_options::options_description behaviorOptions("Behavior options");
behaviorOptions.add_options()
("disable_cuda", "Disable cuda, by default enabled if available")
("max_num_threads", boost::program_options::value< uint32_t >(),
"Select maximum number of threads")
;
// Data Options
boost::program_options::options_description dataOptions("Data options");
dataOptions.add_options()
("file_type", boost::program_options::value< DataHandler::file_type_t >(),
"Select file type, required")
("data_file", boost::program_options::value< DataHandler::file_args_t >()->multitoken(),
"File arguments, required")
("cube_level", boost::program_options::value< level_t >(),
"Select cube level")
("brick_level", boost::program_options::value< level_t >(),
"Select brick level")
("cube_inc", boost::program_options::value< uint32_t >(),
"Select cube inc")
("brick_inc", boost::program_options::value< uint32_t >(),
"Select brick inc")
("cube_cache_size", boost::program_options::value< uint32_t >(),
"Select cube cache size in MB")
("brick_cache_size", boost::program_options::value< uint32_t >(),
"Select brick cache size in MB")
("octree_file", boost::program_options::value< std::string >(),
"Octree file")
("octree_level", boost::program_options::value< level_t >(),
"Select octree level, by default equal to nLevels")
("isos", boost::program_options::value< std::vector< float > >()->multitoken(),
"Set of Isosurfaces")
;
// Other Options
boost::program_options::options_description otherOptions("Other options");
otherOptions.add_options()
("output_file", boost::program_options::value< std::string >(),
"Output file")
;
cmdOptions.add(generalOptions).add(behaviorOptions).add(dataOptions).add(otherOptions);
boost::program_options::variables_map vm;
try
{
boost::program_options::store(
boost::program_options::parse_command_line( ac, av, cmdOptions ), vm );
boost::program_options::notify( vm );
}
catch(...)
{
std::cout << cmdOptions << std::endl;
printHelp();
return false;
}
// General Options
if( vm.count( "help" ) )
{
std::cout << cmdOptions << std::endl;
printHelp();
return false;
}
// Behavior Options
#ifdef IV_USE_CUDA
if( !vm.count( "disable_cuda" ) )
global.useCuda();
#endif
if( vm.count( "max_num_threads" ) )
{
global.setMaxNumThreads( vm["max_num_threads"].as< uint32_t >() );
}
// Data parameters required
if( !vm.count( "file_type" ) ||
!vm.count( "data_file" ) )
{
std::cout << cmdOptions << std::endl;
printHelp();
return false;
}
else
{
const DataHandler::file_type_t fileType = vm["file_type"].as<DataHandler::file_type_t>();
const DataHandler::file_args_t dataParam = vm["data_file"].as< DataHandler::file_args_t >();
switch( fileType )
{
case IV_FILE_TYPE_HDF5:
if( dataParam.size() < 2 )
{
std::cout << cmdOptions << std::endl;
printHelp();
return false;
}
break;
case IV_FILE_TYPE_IVD:
if( dataParam.size() < 1 )
{
std::cout << cmdOptions << std::endl;
printHelp();
return false;
}
break;
case IV_FILE_TYPE_TEST:
if( dataParam.size() < 1 )
{
std::cout << cmdOptions << std::endl;
printHelp();
return false;
}
break;
default:
std::cout << cmdOptions << std::endl;
printHelp();
return false;
}
global.setFileType( fileType );
global.setFileArgs( dataParam );
}
DataHandler::FileHandlerPtr file =
DataHandler::FactoryFileHandler::CreateFileHandler( global.getFileType(),
global.getFileArgs() );
if( !file )
return false;
const level_t nLevels = file->getnLevels();
global.setnLevels( nLevels );
// Data parameters optional
if( vm.count( "cube_inc" ) )
global.setCubeInc( vm["cube_inc"].as< uint32_t >() );
if( vm.count( "brick_inc" ) )
global.setBrickInc( vm["brick_inc"].as< uint32_t >() );
if( vm.count( "cube_cache_size" ) )
global.setCacheSizeCPU( vm["cube_cache_size"].as< uint32_t >() );
if( vm.count( "brick_cache_size" ) )
global.setCacheSizeGPU( vm["brick_cache_size"].as< uint32_t >() );
if( vm.count( "cube_level" ) )
global.setCubeLevel( vm["cube_level"].as< level_t >() );
else // By default 64
global.setCubeLevel( nLevels - 6 );
#ifdef IV_USE_CUDA
if( vm.count( "brick_level" ) )
global.setBrickLevel( vm["brick_level"].as< level_t >() );
else // By default 32
global.setBrickLevel( nLevels - 5 );
if( global.getBrickLevel() < global.getCubeLevel() )
{
std::cout << "Brick level must be >= Cube level" << std::endl;
std::cout << cmdOptions << std::endl;
printHelp();
}
#endif
if( vm.count( "octree_file" ) )
global.setOctreeFile( vm["octree_file"].as< std::string >() );
if( vm.count( "octree_level" ) )
global.setOctreeLevel( vm["octree_level"].as< level_t >() );
else // By default nLevels
global.setOctreeLevel( nLevels );
if( vm.count( "isos" ) )
{
std::vector< float > i = vm["isos"].as< std::vector< float > >();
std::set< float > isos( i.begin(), i.end() );
global.setIsosurfaces( isos );
}
if( vm.count("output_file" ) )
global.setOutputFile( vm["output_file"].as< std::string >() );
return true;
}
