Format the code and improve comments. (1cba6dfc) · Commits · github_fork / Chromap

src/chromap.cc

+35 −29

Original line number	Diff line number	Diff line
		@@ -965,6 +965,7 @@ template <typename MappingRecord>
		void Chromap<MappingRecord>::PostProcessingInLowMemory(
		uint32_t num_mappings_in_mem, uint32_t num_reference_sequences,
		const SequenceBatch &reference) {
		// First, process the mappings in the memory and save them on disk.
		if (num_mappings_in_mem > 0) {
		TempMappingFileHandle<MappingRecord> temp_mapping_file_handle;
		temp_mapping_file_handle.file_path =
		@@ -983,10 +984,13 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		mappings_on_diff_ref_seqs_[i].clear();
		}
		}

		if (temp_mapping_file_handles_.size() == 0) {
		return;
		}

		double sort_and_dedupe_start_time = Chromap<>::GetRealTime();

		// Calculate block size and initialize
		uint64_t max_mem_size = 10 * ((uint64_t)1 << 30);
		if (mapping_output_format_ == MAPPINGFORMAT_SAM \|\|
		@@ -1003,7 +1007,8 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		temp_mapping_file_handles_[hi].LoadTempMappingBlock(
		num_reference_sequences);
		}
		// Merge and dedupe

		// Merge and dedupe.
		bool all_merged = false;
		uint32_t last_rid = std::numeric_limits<uint32_t>::max();
		MappingRecord last_mapping;
		@@ -1013,11 +1018,13 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		uint64_t num_mappings_passing_filters = 0;
		std::vector<MappingRecord> temp_dups_for_bulk_level_dedup;
		temp_dups_for_bulk_level_dedup.reserve(255);

		while (!all_merged) {
		// Merge, dedupe and output
		// Find min first (sorted by rid and then barcode and then positions)
		// Merge, dedupe and output.
		// Find min first (sorted by rid and then barcode and then positions).
		size_t min_handle_index = temp_mapping_file_handles_.size();
		uint32_t min_rid = std::numeric_limits<uint32_t>::max();

		for (size_t hi = 0; hi < temp_mapping_file_handles_.size(); ++hi) {
		TempMappingFileHandle<MappingRecord> &current_handle =
		temp_mapping_file_handles_[hi];
		@@ -1034,7 +1041,8 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		}
		}
		}
		// Append current min to mappings if not a duplicate

		// Append current min to mappings if not a duplicate.
		if (!remove_pcr_duplicates_ \|\|
		min_handle_index != temp_mapping_file_handles_.size()) {
		MappingRecord &current_min_mapping =
		@@ -1062,7 +1070,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		if (!is_bulk_data_ && remove_pcr_duplicates_at_bulk_level_ &&
		temp_dups_for_bulk_level_dedup.size() > 0) {
		// Find the best barcode, break ties first by the number of the
		// barcodes in the dups, then by the barcode abundance
		// barcodes in the dups, then by the barcode abundance.
		last_mapping = temp_dups_for_bulk_level_dedup[0];
		khiter_t barcode_whitelist_lookup_table_iterator =
		kh_get(k64_seq, barcode_whitelist_lookup_table_,
		@@ -1094,16 +1102,13 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		}
		temp_dups_for_bulk_level_dedup.clear();
		}

		if (last_mapping.mapq_ >= mapq_threshold_) {
		// if (allocate_multi_mappings_ \|\| (only_output_unique_mappings_ &&
		// last_mapping.is_unique == 1)) {
		last_mapping.num_dups_ = std::min(
		(uint32_t)std::numeric_limits<uint8_t>::max(), dup_count);
		if (Tn5_shift_) {
		// last_mapping.fragment_start_position += 4;
		// last_mapping.positive_alignment_length -= 4;
		// last_mapping.fragment_length -= 9;
		// last_mapping.negative_alignment_length -= 5;
		last_mapping.Tn5Shift();
		}
		output_tools_.AppendMapping(last_rid, reference, last_mapping);
		@@ -1127,6 +1132,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		temp_mapping_file_handles_[min_handle_index].Next(
		num_reference_sequences);
		}

		// Check if all are merged.
		all_merged = true;
		for (size_t hi = 0; hi < temp_mapping_file_handles_.size(); ++hi) {
		@@ -1135,11 +1141,12 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		}
		}
		}

		if (last_mapping.mapq_ >= mapq_threshold_) {
		if (!is_bulk_data_ && remove_pcr_duplicates_at_bulk_level_ &&
		temp_dups_for_bulk_level_dedup.size() > 0) {
		// Find the best barcode, break ties first by the number of the barcodes
		// in the dups, then by the barcode abundance
		// in the dups, then by the barcode abundance.
		last_mapping = temp_dups_for_bulk_level_dedup[0];
		khiter_t barcode_whitelist_lookup_table_iterator = kh_get(
		k64_seq, barcode_whitelist_lookup_table_, last_mapping.GetBarcode());
		@@ -1173,26 +1180,25 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		last_mapping.num_dups_ =
		std::min((uint32_t)std::numeric_limits<uint8_t>::max(), dup_count);
		if (Tn5_shift_) {
		// last_mapping.fragment_start_position += 4;
		// last_mapping.positive_alignment_length -= 4;
		// last_mapping.fragment_length -= 9;
		// last_mapping.negative_alignment_length -= 5;
		last_mapping.Tn5Shift();
		}
		output_tools_.AppendMapping(last_rid, reference, last_mapping);
		++num_mappings_passing_filters;
		//}
		}

		if (last_mapping.is_unique_ == 1) {
		++num_uni_mappings;
		} else {
		++num_multi_mappings;
		}
		// Delete temp files

		// Delete temp files.
		for (size_t hi = 0; hi < temp_mapping_file_handles_.size(); ++hi) {
		temp_mapping_file_handles_[hi].FinalizeTempMappingLoading();
		remove(temp_mapping_file_handles_[hi].file_path.c_str());
		}

		if (remove_pcr_duplicates_) {
		std::cerr << "Sorted, deduped and outputed mappings in "
		<< Chromap<>::GetRealTime() - sort_and_dedupe_start_time
		@@ -2782,8 +2788,8 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		static uint64_t thread_num_uniquely_mapped_reads = 0;
		static uint64_t thread_num_barcode_in_whitelist = 0;
		static uint64_t thread_num_corrected_barcode = 0;
		#pragma omp threadprivate(thread_num_candidates, thread_num_mappings, \
		thread_num_mapped_reads, \
		#pragma omp threadprivate( \
		thread_num_candidates, thread_num_mappings, thread_num_mapped_reads, \
		thread_num_uniquely_mapped_reads, thread_num_barcode_in_whitelist, \
		thread_num_corrected_barcode)
		double real_start_mapping_time = Chromap<>::GetRealTime();
		@@ -2856,7 +2862,6 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		#pragma omp taskloop num_tasks(num_threads_ *num_threads_)
		for (uint32_t read_index = 0; read_index < num_loaded_reads;
		++read_index) {

		bool current_barcode_is_whitelisted = true;
		if (!barcode_whitelist_file_path_.empty()) {
		current_barcode_is_whitelisted = CorrectBarcodeAt(
		@@ -5951,8 +5956,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		"Output mappings in pairs format (defined by 4DN for HiC data)")(
		"pairs-natural-chr-order",
		"natural chromosome order for pairs flipping",
		cxxopts::value<std::string>(), "FILE")
		("barcode-translate",
		cxxopts::value<std::string>(),
		"FILE")("barcode-translate",
		"Convert barcode to the specified sequences during output",
		cxxopts::value<std::string>(), "FILE");
		//("PAF", "Output mappings in PAF format (only for test)");
		@@ -6259,7 +6264,8 @@ void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		}

		if (result.count("barcode-translate")) {
		mapping_parameters.barcode_translate_table_path = result["barcode-translate"].as<std::string>();
		mapping_parameters.barcode_translate_table_path =
		result["barcode-translate"].as<std::string>();
		}

		if (result.count("skip-barcode-check")) {

src/mapping.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -6,7 +6,7 @@ namespace chromap {
		// An interface for various mapping formats.
		class Mapping {
		public:
		Mapping() {}
		virtual ~Mapping() = default;
		//// Defines the orders of mappings. Sort by mapping positions first, then
		//// sorted by barcode and other fields if available. Make sure to consider
		//// enough field so that the order is always deterministic.

src/temp_mapping.h

+6 −2

Original line number	Diff line number	Diff line
		@@ -29,8 +29,9 @@ struct TempMappingFileHandle {
		uint32_t current_mapping_index;
		uint32_t num_mappings_on_current_rid;
		uint32_t num_loaded_mappings_on_current_rid;
		std::vector<MappingRecord>
		mappings; // this vector only keep mappings on the same ref seq
		// This vector only keep mappings on the same ref seq.
		std::vector<MappingRecord> mappings;

		inline void InitializeTempMappingLoading(uint32_t num_reference_sequences) {
		file = fopen(file_path.c_str(), "rb");
		assert(file != NULL);
		@@ -42,7 +43,9 @@ struct TempMappingFileHandle {
		// std::cerr << "Block size: " << block_size << ", initialize temp file " <<
		// file_path << "\n";
		}

		inline void FinalizeTempMappingLoading() { fclose(file); }

		inline void LoadTempMappingBlock(uint32_t num_reference_sequences) {
		num_mappings = 0;
		while (num_mappings == 0) {
		@@ -82,6 +85,7 @@ struct TempMappingFileHandle {
		}
		current_mapping_index = 0;
		}

		inline void Next(uint32_t num_reference_sequences) {
		++current_mapping_index;
		if (current_mapping_index >= num_mappings) {

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