Rename the variables for clearer meaninig. (3da88920) · Commits · github_fork / Chromap

src/chromap.h

+10 −9

Original line number	Diff line number	Diff line
		@@ -172,8 +172,8 @@ void Chromap::MapSingleEndReads() {
		SequenceBatch reference;
		reference.InitializeLoading(mapping_parameters_.reference_file_path);
		uint32_t num_reference_sequences = reference.LoadAllSequences();
		if (mapping_parameters_.custom_rid_order_path.length() > 0) {
		GenerateCustomRidRanks(mapping_parameters_.custom_rid_order_path,
		if (mapping_parameters_.custom_rid_order_file_path.length() > 0) {
		GenerateCustomRidRanks(mapping_parameters_.custom_rid_order_file_path,
		num_reference_sequences, reference,
		custom_rid_rank_);
		reference.ReorderSequences(custom_rid_rank_);
		@@ -340,7 +340,7 @@ void Chromap::MapSingleEndReads() {
		mapping_metadata.minimizers_);

		if (mapping_metadata.minimizers_.size() > 0) {
		if (mapping_parameters_.custom_rid_order_path.length() > 0) {
		if (mapping_parameters_.custom_rid_order_file_path.length() > 0) {
		RerankCandidatesRid(mapping_metadata.positive_candidates_);
		RerankCandidatesRid(mapping_metadata.negative_candidates_);
		}
		@@ -541,16 +541,16 @@ void Chromap::MapPairedEndReads() {
		SequenceBatch reference;
		reference.InitializeLoading(mapping_parameters_.reference_file_path);
		uint32_t num_reference_sequences = reference.LoadAllSequences();
		if (mapping_parameters_.custom_rid_order_path.length() > 0) {
		GenerateCustomRidRanks(mapping_parameters_.custom_rid_order_path,
		if (mapping_parameters_.custom_rid_order_file_path.length() > 0) {
		GenerateCustomRidRanks(mapping_parameters_.custom_rid_order_file_path,
		num_reference_sequences, reference,
		custom_rid_rank_);
		reference.ReorderSequences(custom_rid_rank_);
		}
		if (mapping_parameters_.mapping_output_format == MAPPINGFORMAT_PAIRS) {
		GenerateCustomRidRanks(mapping_parameters_.pairs_custom_rid_order_path,
		num_reference_sequences, reference,
		pairs_custom_rid_rank_);
		GenerateCustomRidRanks(
		mapping_parameters_.pairs_flipping_custom_rid_order_file_path,
		num_reference_sequences, reference, pairs_custom_rid_rank_);
		}

		// Load index
		@@ -844,7 +844,8 @@ void Chromap::MapPairedEndReads() {
		thread_num_candidates +=
		current_num_candidates1 + current_num_candidates2;

		if (mapping_parameters_.custom_rid_order_path.length() > 0) {
		if (mapping_parameters_.custom_rid_order_file_path.length() >
		0) {
		RerankCandidatesRid(
		paired_end_mapping_metadata.mapping_metadata1_
		.positive_candidates_);

src/chromap_driver.cc

+2 −2

Original line number	Diff line number	Diff line
		@@ -411,12 +411,12 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		}

		if (result.count("chr-order")) {
		mapping_parameters.custom_rid_order_path =
		mapping_parameters.custom_rid_order_file_path =
		result["chr-order"].as<std::string>();
		}

		if (result.count("pairs-natural-chr-order")) {
		mapping_parameters.pairs_custom_rid_order_path =
		mapping_parameters.pairs_flipping_custom_rid_order_file_path =
		result["pairs-natural-chr-order"].as<std::string>();
		}

src/mapping_parameters.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -59,9 +59,9 @@ struct MappingParameters {
		std::string mapping_output_file_path;
		std::string matrix_output_prefix;
		// The order for general sorting.
		std::string custom_rid_order_path;
		std::string custom_rid_order_file_path;
		// The order for pairs format flipping.
		std::string pairs_custom_rid_order_path;
		std::string pairs_flipping_custom_rid_order_file_path;
		std::string barcode_translate_table_file_path;
		bool skip_barcode_check = false;

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