Minor change on mapping stats output function. (824f0ce6) · Commits · github_fork / Chromap

src/chromap.cc

+5 −15

Original line number	Diff line number	Diff line
		@@ -1108,7 +1108,6 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		mappings_on_diff_ref_seqs);
		std::cerr << "After removing PCR duplications, ";
		OutputMappingStatistics(num_reference_sequences,
		mappings_on_diff_ref_seqs,
		mappings_on_diff_ref_seqs);
		} else {
		mapping_processor.SortOutputMappings(num_reference_sequences,
		@@ -1123,7 +1122,6 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		multi_mapping_allocation_distance_, mappings_on_diff_ref_seqs);
		std::cerr << "After allocating multi-mappings, ";
		OutputMappingStatistics(num_reference_sequences,
		mappings_on_diff_ref_seqs,
		mappings_on_diff_ref_seqs);
		mapping_processor.SortOutputMappings(num_reference_sequences,
		mappings_on_diff_ref_seqs);
		@@ -1499,7 +1497,6 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		mappings_on_diff_ref_seqs);
		std::cerr << "After removing PCR duplications, ";
		OutputMappingStatistics(num_reference_sequences,
		mappings_on_diff_ref_seqs,
		mappings_on_diff_ref_seqs);
		} else {
		mapping_processor.SortOutputMappings(num_reference_sequences,
		@@ -1514,7 +1511,6 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		multi_mapping_allocation_distance_, mappings_on_diff_ref_seqs);
		std::cerr << "After allocating multi-mappings, ";
		OutputMappingStatistics(num_reference_sequences,
		mappings_on_diff_ref_seqs,
		mappings_on_diff_ref_seqs);
		mapping_processor.SortOutputMappings(num_reference_sequences,
		mappings_on_diff_ref_seqs);
		@@ -1608,20 +1604,14 @@ void Chromap<MappingRecord>::OutputMappingStatistics() {
		template <typename MappingRecord>
		void Chromap<MappingRecord>::OutputMappingStatistics(
		uint32_t num_reference_sequences,
		const std::vector<std::vector<MappingRecord>> &uni_mappings,
		const std::vector<std::vector<MappingRecord>> &multi_mappings) {
		const std::vector<std::vector<MappingRecord>> &mappings_on_diff_ref_seqs) {
		uint64_t num_uni_mappings = 0;
		uint64_t num_multi_mappings = 0;
		for (auto &uni_mappings_on_one_ref_seq : uni_mappings) {
		for (auto &uni_mapping : uni_mappings_on_one_ref_seq) {
		if ((uni_mapping.is_unique_) == 1) {
		for (auto &mappings_on_one_ref_seq : mappings_on_diff_ref_seqs) {
		for (auto &mapping : mappings_on_one_ref_seq) {
		if ((mapping.is_unique_) == 1) {
		++num_uni_mappings;
		}
		}
		}
		for (auto &multi_mappings_on_one_ref_seq : multi_mappings) {
		for (auto &multi_mapping : multi_mappings_on_one_ref_seq) {
		if ((multi_mapping.is_unique_) != 1) {
		} else {
		++num_multi_mappings;
		}
		}

src/chromap.h

+3 −4

Original line number	Diff line number	Diff line
		@@ -172,10 +172,9 @@ class Chromap {

		void OutputMappingStatistics();

		void OutputMappingStatistics(
		uint32_t num_reference_sequences,
		const std::vector<std::vector<MappingRecord> > &uni_mappings,
		const std::vector<std::vector<MappingRecord> > &multi_mappings);
		void OutputMappingStatistics(uint32_t num_reference_sequences,
		const std::vector<std::vector<MappingRecord> >
		&mappings_on_diff_ref_seqs);

		void GenerateCustomizedRidRank(const std::string &rid_order_path,
		const SequenceBatch &reference,

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