Use a func to add indexing options. (c55b92c9) · Commits · github_fork / Chromap

src/chromap_driver.cc

+19 −9

Original line number	Diff line number	Diff line
		@@ -9,16 +9,25 @@
		#include "cxxopts.hpp"

		namespace chromap {
		namespace {

		void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		cxxopts::Options options(
		"chromap", "Fast alignment and preprocessing of chromatin profiles");
		void AddIndexingOptions(cxxopts::Options &options) {
		options.add_options("Indexing")("i,build-index", "Build index")(
		"min-frag-length",
		"Min fragment length for choosing k and w automatically [30]",
		cxxopts::value<int>(),
		"INT")("k,kmer", "Kmer length [17]", cxxopts::value<int>(), "INT")(
		"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",
		@@ -120,8 +129,9 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		cxxopts::value<std::string>(),
		"FILE")("barcode-translate",
		"Convert barcode to the specified sequences during output",
		cxxopts::value<std::string>(), "FILE")
		("summary", "Summarize the mapping statistics at bulk or barcode level",
		cxxopts::value<std::string>(), "FILE")(
		"summary",
		"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");