Use separate functions to add options. (47dfb47d) · Commits · github_fork / Chromap

src/chromap_driver.cc

+51 −29

Original line number	Diff line number	Diff line
		@@ -20,17 +20,9 @@ void AddIndexingOptions(cxxopts::Options &options) {
		"w,window", "Window size [7]", cxxopts::value<int>(), "INT");
		}

		} // namespace

		void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		cxxopts::Options options(
		"chromap", "Fast alignment and preprocessing of chromatin profiles");

		AddIndexingOptions(options);

		options.set_width(120).add_options("Mapping")
		//("m,map", "Map reads")
		("preset",
		void AddMappingOptions(cxxopts::Options &options) {
		options.set_width(120).add_options("Mapping")(
		"preset",
		"Preset parameters for mapping reads (always applied before other "
		"options) []\natac: mapping ATAC-seq/scATAC-seq reads\nchip: mapping "
		"ChIP-seq reads\nhic: mapping Hi-C reads",
		@@ -83,16 +75,9 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		cxxopts::value<double>(),
		"FLT")("t,num-threads", "# threads for mapping [1]",
		cxxopts::value<int>(), "INT");
		// options.add_options("Peak")
		// ("cell-by-bin", "Generate cell-by-bin matrix")
		// ("bin-size", "Bin size to generate cell-by-bin matrix [5000]",
		// cxxopts::value<int>(), "INT")
		// ("depth-cutoff", "Depth cutoff for peak calling [3]",
		// cxxopts::value<int>(), "INT")
		// ("peak-min-length", "Min length of peaks to report [30]",
		// cxxopts::value<int>(), "INT")
		// ("peak-merge-max-length", "Peaks within this length will be merged [30]",
		// cxxopts::value<int>(), "INT");
		}

		void AddInputOptions(cxxopts::Options &options) {
		options.add_options("Input")("r,ref", "Reference file",
		cxxopts::value<std::string>(), "FILE")(
		"x,index", "Index file", cxxopts::value<std::string>(), "FILE")(
		@@ -108,6 +93,9 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		"Format for read files and barcode files [\"r1:0:-1,bc:0:-1\" "
		"as 10x Genomics single-end format]",
		cxxopts::value<std::string>(), "STR");
		}

		void AddOutputOptions(cxxopts::Options &options) {
		options.add_options("Output")("o,output", "Output file",
		cxxopts::value<std::string>(), "FILE")
		//("p,matrix-output-prefix", "Prefix of matrix output files",
		@@ -134,7 +122,9 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		"Summarize the mapping statistics at bulk or barcode level",
		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");
		}

		void AddDevelopmentOptions(cxxopts::Options &options) {
		options.add_options("Development options")("A,match-score", "Match score [1]",
		cxxopts::value<int>(), "INT")(
		"B,mismatch-penalty", "Mismatch penalty [4]", cxxopts::value<int>(),
		@@ -157,6 +147,38 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		"PAF", "Output mappings in PAF format (only for test)")(
		"skip-barcode-check",
		"Do not check whether too few barcodes are in the whitelist");
		}

		void AddPeakOptions(cxxopts::Options &options) {
		options.add_options("Peak")("cell-by-bin", "Generate cell-by-bin matrix")(
		"bin-size", "Bin size to generate cell-by-bin matrix [5000]",
		cxxopts::value<int>(),
		"INT")("depth-cutoff", "Depth cutoff for peak calling [3]",
		cxxopts::value<int>(),
		"INT")("peak-min-length", "Min length of peaks to report [30]",
		cxxopts::value<int>(), "INT")(
		"peak-merge-max-length", "Peaks within this length will be merged [30]",
		cxxopts::value<int>(), "INT");
		}

		} // namespace

		void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		cxxopts::Options options(
		"chromap", "Fast alignment and preprocessing of chromatin profiles");

		options.add_options()("v,version", "Print version")("h,help", "Print help");

		AddIndexingOptions(options);
		AddMappingOptions(options);

		// We don't support peak options for now.
		// AddPeakOptions(options);

		AddInputOptions(options);
		AddOutputOptions(options);

		AddDevelopmentOptions(options);

		auto result = options.parse(argc, argv);
		if (result.count("h")) {

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