Function main

Consensus/Consensus.cpp:461–508

}

int main(int argc, char** argv)
{
	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 'v': opt::verbose++; break;
			case 'o': arg >> opt::outPath; break;
			case 'p': arg >> opt::pileupPath; break;
			case 'V': opt::onlyVariants = true; break;
			case OPT_HELP:
				cout << USAGE_MESSAGE;
				exit(EXIT_SUCCESS);
			case OPT_VERSION:
				cout << VERSION_MESSAGE;
				exit(EXIT_SUCCESS);
		}
		if (optarg != NULL && !arg.eof()) {
			cerr << PROGRAM ": invalid option: `-"
				<< (char)c << optarg << "'\n";
			exit(EXIT_FAILURE);
		}
	}

	if (opt::outPath.empty() && opt::pileupPath.empty()) {
		cerr << PROGRAM ": " << "missing -o,--out option\n";
		die = true;
	}

	if (argc - optind < 1) {
		cerr << PROGRAM ": missing arguments\n";
		die = true;
	} else if (argc - optind > 1) {
		cerr << PROGRAM ": too many arguments\n";
		die = true;
	}
	if (die) {
		cerr << "Try `" << PROGRAM
			<< " --help' for more information.\n";
		exit(EXIT_FAILURE);
	}

	readContigs(argv[optind++]);
	buildBaseQuality();
	consensus(opt::outPath, opt::pileupPath);
}