Use reference instead of pointer as func parameters. (001d2ff2) · Commits · github_fork / Chromap

src/chromap.cc

+9 −10

Original line number	Diff line number	Diff line
		@@ -1252,7 +1252,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		// Handle output
		num_mappings_in_mem += MoveMappingsInBuffersToMappingContainer(
		num_reference_sequences,
		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		if (low_memory_mode_ &&
		num_mappings_in_mem > max_num_mappings_in_mem) {
		TempMappingFileHandle<MappingRecord> temp_mapping_file_handle;
		@@ -2415,7 +2415,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		{
		MoveMappingsInBuffersToMappingContainer(
		num_reference_sequences,
		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		}
		std::cerr << "Mapped in " << GetRealTime() - real_batch_start_time
		<< "s.\n";
		@@ -3131,23 +3131,22 @@ template <typename MappingRecord>
		uint32_t Chromap<MappingRecord>::MoveMappingsInBuffersToMappingContainer(
		uint32_t num_reference_sequences,
		std::vector<std::vector<std::vector<MappingRecord>>>
		*mappings_on_diff_ref_seqs_for_diff_threads_for_saving) {
		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving) {
		// double real_start_time = Chromap<>::GetRealTime();
		uint32_t num_moved_mappings = 0;
		for (int ti = 0; ti < num_threads_; ++ti) {
		for (uint32_t i = 0; i < num_reference_sequences; ++i) {
		num_moved_mappings +=
		(*mappings_on_diff_ref_seqs_for_diff_threads_for_saving)[ti][i]
		.size();
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i].size();
		mappings_on_diff_ref_seqs_[i].insert(
		mappings_on_diff_ref_seqs_[i].end(),
		std::make_move_iterator(
		(*mappings_on_diff_ref_seqs_for_diff_threads_for_saving)[ti][i]
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i]
		.begin()),
		std::make_move_iterator(
		(*mappings_on_diff_ref_seqs_for_diff_threads_for_saving)[ti][i]
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i]
		.end()));
		(*mappings_on_diff_ref_seqs_for_diff_threads_for_saving)[ti][i].clear();
		mappings_on_diff_ref_seqs_for_diff_threads_for_saving[ti][i].clear();
		}
		}
		// std::cerr << "Moved mappings in " << Chromap<>::GetRealTime() -

src/chromap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -340,7 +340,7 @@ class Chromap {
		uint32_t MoveMappingsInBuffersToMappingContainer(
		uint32_t num_reference_sequences,
		std::vector<std::vector<std::vector<MappingRecord> > >
		*mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		&mappings_on_diff_ref_seqs_for_diff_threads_for_saving);
		void OutputBarcodeStatistics();
		void OutputMappingStatistics();
		void OutputMappingStatistics(

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