use a driver class to simplify main (89d61ef3) · Commits · github_fork / Chromap

Makefile

+2 −2

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@ objs_dir=objs
		objs+=$(patsubst %.cc,$(objs_dir)/%.o,$(cpp_source))

		cxx=g++
		cxxflags=-std=c++11 -Wall -O3 -funroll-all-loops -fopenmp -march=native
		cxxflags=-std=c++11 -Wall -O3 -fopenmp -march=native
		ldflags=-lm -lz

		exec=chromap

+8 −3

Original line number	Diff line number	Diff line
		@@ -1488,9 +1488,8 @@ uint8_t Chromap<MappingRecord>::GetMAPQ(int num_positive_candidates, int num_neg
		mapq <<= 1;
		return (uint8_t)mapq;
		}
		} // namespace chromap

		int main(int argc, char *argv[]) {
		void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		cxxopts::Options options("chromap", "A short read mapper for chromatin biology");
		options.add_options("Indexing")
		("i,build-index", "Build index")
		@@ -1777,5 +1776,11 @@ int main(int argc, char *argv[]) {
		} else {
		std::cerr << options.help({"", "Indexing", "Mapping", "Input", "Output"});
		}
		}
		} // namespace chromap

		int main(int argc, char *argv[]) {
		chromap::ChromapDriver chromap_driver;
		chromap_driver.ParseArgsAndRun(argc, argv);
		return 0;
		}

+8 −0

Original line number	Diff line number	Diff line
		@@ -38,6 +38,14 @@ enum Direction {

		#define SortMappingWithoutBarcode(m) (((((m).fragment_start_position<<16)\|(m).fragment_length)<<8)\|(m).mapq)
		//#define SortMappingWithoutBarcode(m) (m)

		class ChromapDriver {
		public:
		ChromapDriver() {}
		~ChromapDriver() {}
		void ParseArgsAndRun(int argc, char *argv[]);
		};

		template <typename MappingRecord = MappingWithoutBarcode>
		class Chromap {
		public: