Use reference to make code easier to read. (560e286a) · Commits · github_fork / Chromap

src/chromap.h

+2 −4

Original line number	Diff line number	Diff line
		@@ -219,7 +219,7 @@ void Chromap::MapSingleEndReads() {

		MappingWriter<MappingRecord> mapping_writer(mapping_parameters_,
		barcode_length_,
		/custom_rid_rank=/nullptr);
		pairs_custom_rid_rank_);

		mapping_writer.OutputHeader(num_reference_sequences, reference);

		@@ -609,9 +609,7 @@ void Chromap::MapPairedEndReads() {

		MappingWriter<MappingRecord> mapping_writer(
		mapping_parameters_, barcode_length_,
		mapping_parameters_.mapping_output_format == MAPPINGFORMAT_PAIRS
		? &pairs_custom_rid_rank_
		: nullptr);
		pairs_custom_rid_rank_);
		mapping_writer.OutputHeader(num_reference_sequences, reference);

		uint32_t num_mappings_in_mem = 0;

+1 −12

Original line number	Diff line number	Diff line
		@@ -29,6 +29,7 @@ template <typename MappingRecord>
		class MappingGenerator {
		public:
		MappingGenerator() = delete;

		MappingGenerator(const MappingParameters &mapping_parameters,
		const std::vector<int> &pairs_custom_rid_rank)
		: mapping_parameters_(mapping_parameters),
		@@ -199,19 +200,7 @@ class MappingGenerator {
		int force_mapq, uint8_t &mapq1, uint8_t &mapq2);

		const MappingParameters mapping_parameters_;
		// const int error_threshold_;
		const int NUM_VPU_LANES_;
		// const int match_score_;
		// const int mismatch_penalty_;
		// const std::vector<int> gap_open_penalties_;
		// const std::vector<int> gap_extension_penalties_;
		// const int max_num_best_mappings_;
		// const int max_insert_size_;
		// const int min_read_length_;
		// const int drop_repetitive_reads_;
		// const bool is_bulk_data_;
		// const bool split_alignment_;
		// const MappingOutputFormat mapping_output_format_;
		const std::vector<int> pairs_custom_rid_rank_;
		};

+2 −3

Original line number	Diff line number	Diff line
		@@ -31,11 +31,10 @@ class MappingWriter {

		MappingWriter(const MappingParameters mapping_parameters,
		const uint32_t cell_barcode_length,
		const std::vector<int> *custom_rid_rank)
		const std::vector<int> &custom_rid_rank)
		: mapping_parameters_(mapping_parameters),
		cell_barcode_length_(cell_barcode_length),
		custom_rid_rank_(custom_rid_rank != nullptr ? *custom_rid_rank
		: std::vector<int>()) {
		custom_rid_rank_(custom_rid_rank) {
		if (!mapping_parameters_.barcode_translate_table_file_path.empty()) {
		barcode_translator_.SetTranslateTable(
		mapping_parameters_.barcode_translate_table_file_path);