Function main

MergePaths/MergeContigs.cpp:434–661

}

int
main(int argc, char** argv)
{
	opt::trimMasked = false;

	string commandLine;
	{
		ostringstream ss;
		char** last = argv + argc - 1;
		copy(argv, last, ostream_iterator<const char*>(ss, " "));
		ss << *last;
		commandLine = ss.str();
	}

	if (!opt::db.empty())
		opt::metaVars.resize(3);

	bool die = false;
	for (int c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) {
		istringstream arg(optarg != NULL ? optarg : "");
		switch (c) {
		case '?':
			die = true;
			break;
		case 'g':
			arg >> opt::graphPath;
			break;
		case 'k':
			arg >> opt::k;
			break;
		case 'o':
			arg >> opt::out;
			break;
		case 'v':
			opt::verbose++;
			break;
		case OPT_HELP:
			cout << USAGE_MESSAGE;
			exit(EXIT_SUCCESS);
		case OPT_VERSION:
			cout << VERSION_MESSAGE;
			exit(EXIT_SUCCESS);
		case OPT_DB:
			arg >> opt::db;
			break;
		case OPT_LIBRARY:
			arg >> opt::metaVars[0];
			break;
		case OPT_STRAIN:
			arg >> opt::metaVars[1];
			break;
		case OPT_SPECIES:
			arg >> opt::metaVars[2];
			break;
		}
		if (optarg != NULL && !arg.eof()) {
			cerr << PROGRAM ": invalid option: `-" << (char)c << optarg << "'\n";
			exit(EXIT_FAILURE);