Use struct to hold index parameters. (46072416) · Commits · github_fork / Chromap

src/chromap.cc

+17 −23

Original line number	Diff line number	Diff line
		@@ -6029,10 +6029,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		return;
		}
		// Parameters and their default
		IndexParameters index_parameters;
		MappingParameters mapping_parameters;
		int min_fragment_length = 30;
		int kmer_size = 17;
		int window_size = 7;

		if (result.count("preset")) {
		std::string read_type = result["preset"].as<std::string>();
		@@ -6065,23 +6063,23 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		}
		// Optional parameters
		if (result.count("min-frag-length")) {
		min_fragment_length = result["min-frag-length"].as<int>();
		int min_fragment_length = result["min-frag-length"].as<int>();
		if (min_fragment_length <= 60) {
		kmer_size = 17;
		window_size = 7;
		index_parameters.kmer_size = 17;
		index_parameters.window_size = 7;
		} else if (min_fragment_length <= 80) {
		kmer_size = 19;
		window_size = 10;
		index_parameters.kmer_size = 19;
		index_parameters.window_size = 10;
		} else {
		kmer_size = 23;
		window_size = 11;
		index_parameters.kmer_size = 23;
		index_parameters.window_size = 11;
		}
		}
		if (result.count("k")) {
		kmer_size = result["kmer"].as<int>();
		index_parameters.kmer_size = result["kmer"].as<int>();
		}
		if (result.count("w")) {
		window_size = result["window"].as<int>();
		index_parameters.window_size = result["window"].as<int>();
		}
		if (result.count("e")) {
		mapping_parameters.error_threshold = result["error-threshold"].as<int>();
		@@ -6232,26 +6230,22 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {

		std::cerr << std::setprecision(2) << std::fixed;
		if (result.count("i")) {
		std::string reference_file_path;
		if (result.count("r")) {
		reference_file_path = result["ref"].as<std::string>();
		index_parameters.reference_file_path = result["ref"].as<std::string>();
		} else {
		chromap::Chromap<>::ExitWithMessage("No reference specified!");
		}
		std::string output_file_path;
		if (result.count("o")) {
		output_file_path = result["output"].as<std::string>();
		index_parameters.index_output_file_path = result["output"].as<std::string>();
		} else {
		chromap::Chromap<>::ExitWithMessage("No output file specified!");
		}
		std::cerr << "Build index for the reference.\n";
		std::cerr << "Kmer length: " << kmer_size
		<< ", window size: " << window_size << "\n";
		std::cerr << "Reference file: " << reference_file_path << "\n";
		std::cerr << "Output file: " << output_file_path << "\n";
		chromap::Chromap<> chromap_for_indexing(
		kmer_size, window_size, /num_threads=/1, reference_file_path,
		output_file_path);
		std::cerr << "Kmer length: " << index_parameters.kmer_size
		<< ", window size: " << index_parameters.window_size << "\n";
		std::cerr << "Reference file: " << index_parameters.reference_file_path << "\n";
		std::cerr << "Output file: " << index_parameters.index_output_file_path << "\n";
		chromap::Chromap<> chromap_for_indexing(index_parameters);
		chromap_for_indexing.ConstructIndex();
		} else if (result.count("1")) {
		std::cerr << "Start to map reads.\n";

src/chromap.h

+14 −8

Original line number	Diff line number	Diff line
		@@ -64,6 +64,14 @@ struct BarcodeWithQual {
		}
		};

		struct IndexParameters {
		int kmer_size = 17;
		int window_size = 7;
		int num_threads = 1;
		std::string reference_file_path;
		std::string index_output_file_path;
		};

		struct MappingParameters {
		int error_threshold = 8;
		int match_score = 1;
		@@ -131,14 +139,12 @@ template <typename MappingRecord = MappingWithoutBarcode>
		class Chromap {
		public:
		// For index construction
		Chromap(int kmer_size, int window_size, int num_threads,
		const std::string &reference_file_path,
		const std::string &index_file_path)
		: kmer_size_(kmer_size),
		window_size_(window_size),
		num_threads_(num_threads),
		reference_file_path_(reference_file_path),
		index_file_path_(index_file_path) {
		Chromap(const IndexParameters &index_parameters)
		: kmer_size_(index_parameters.kmer_size),
		window_size_(index_parameters.window_size),
		num_threads_(index_parameters.num_threads),
		reference_file_path_(index_parameters.reference_file_path),
		index_file_path_(index_parameters.index_output_file_path) {
		barcode_lookup_table_ = NULL;
		barcode_whitelist_lookup_table_ = NULL;
		barcode_histogram_ = NULL;

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