Add version. (957a92b4) · Commits · github_fork / Chromap

src/chromap.cc

+9 −2

Original line number	Diff line number	Diff line
		@@ -4213,6 +4213,7 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		("pairs-natural-chr-order", "natural chromosome order for pairs flipping", cxxopts::value<std::string>(), "FILE");
		//("PAF", "Output mappings in PAF format (only for test)");
		options.add_options()
		("v,version", "Print version")
		("h,help", "Print help");
		options.add_options("Development options")
		("A,match-score", "Match score [1]", cxxopts::value<int>(), "INT")
		@@ -4227,6 +4228,14 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		("PAF", "Output mappings in PAF format (only for test)");

		auto result = options.parse(argc, argv);
		if (result.count("h")) {
		std::cerr << options.help({"", "Indexing", "Mapping", "Peak", "Input", "Output"});
		return;
		}
		if (result.count("v")) {
		std::cerr << CHROMAP_VERSION << "\n";
		return;
		}
		// Parameters and their default
		int min_fragment_length = 30;
		int kmer_size = 17;
		@@ -4655,8 +4664,6 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		}
		}
		}
		} else if (result.count("h")) {
		std::cerr << options.help({"", "Indexing", "Mapping", "Peak", "Input", "Output"});
		} else {
		std::cerr << options.help({"", "Indexing", "Mapping", "Peak", "Input", "Output"});
		}

+2 −0