void
parseChromDepthOptions(
const illumina::Program& prog,
int argc, char* argv[],
ChromDepthOptions& opt)
{
namespace po = boost::program_options;
po::options_description req("configuration");
req.add_options()
("align-file", po::value(&opt.alignmentFilename),
"alignment file in BAM or CRAM format")
("chrom", po::value<chroms_t>(),
"chromosome name. May be supplied more than once. At least one entry required.")
("output-file", po::value(&opt.outputFilename),
"write stats to filename (default: stdout)")
("ref", po::value(&opt.referenceFilename),
"fasta reference sequence (required)")
;
po::options_description help("help");
help.add_options()
("help,h","print this message");
po::options_description visible("options");
visible.add(req).add(help);
bool po_parse_fail(false);
po::variables_map vm;
try
{
po::store(po::parse_command_line(argc, argv, visible,
po::command_line_style::unix_style ^ po::command_line_style::allow_short), vm);
po::notify(vm);
}
catch (const boost::program_options::error& e) // todo:: find out what is the more specific exception class thrown by program options
{
log_os << "\nERROR: Exception thrown by option parser: " << e.what() << "\n";
po_parse_fail=true;
}
if ((argc<=1) || (vm.count("help")) || po_parse_fail)
{
usage(log_os,prog,visible);
log_os << "\n" << prog.name() << ": get chromosome depth from alignment file\n\n";
log_os << "version: " << prog.version() << "\n\n";
log_os << "usage: " << prog.name() << " [options] > stats\n\n";
log_os << visible << "\n";
exit(EXIT_FAILURE);
}
std::string errorMsg;
if (parseOptions(vm, opt, errorMsg))
{
usage(log_os, prog, visible, errorMsg.c_str());
}
}
void
usage(
std::ostream& os,
const illumina::Program& prog,
const boost::program_options::options_description& visible,
const char* desc,
const char* afteropts,
const char* msg)
{
os << "\n" << prog.name() << ": " << desc << "\n\n";
os << "version: " << prog.version() << "\n";
os << "compiler: " << prog.compiler() << "\n";
os << "build-time: " << prog.buildTime() << "\n\n";
os << "usage: " << prog.name() << " [options]" << afteropts << "\n\n";
os << visible << "\n\n";
if (nullptr != msg)
{
os << msg << "\n\n";
}
exit(2);
}