Use reference instead of pointers. (9711b7ad) · Commits · github_fork / Chromap

src/chromap.cc

+6 −6

Original line number	Diff line number	Diff line
		@@ -1266,7 +1266,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {

		uint32_t num_loaded_reads_for_loading = 0;
		uint32_t num_loaded_reads = LoadSingleEndReadsWithBarcodes(
		&read_batch_for_loading, &barcode_batch_for_loading);
		read_batch_for_loading, barcode_batch_for_loading);
		read_batch_for_loading.SwapSequenceBatch(read_batch);

		if (!is_bulk_data_) {
		@@ -1312,7 +1312,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		#pragma omp task
		{
		num_loaded_reads_for_loading = LoadSingleEndReadsWithBarcodes(
		&read_batch_for_loading, &barcode_batch_for_loading);
		read_batch_for_loading, barcode_batch_for_loading);
		} // end of openmp loading task
		// int grain_size = 10000;
		//#pragma omp taskloop grainsize(grain_size) //num_tasks(num_threads_* 50)
		@@ -1532,18 +1532,18 @@ void Chromap<MappingRecord>::MapSingleEndReads() {

		template <typename MappingRecord>
		uint32_t Chromap<MappingRecord>::LoadSingleEndReadsWithBarcodes(
		SequenceBatch read_batch, SequenceBatch barcode_batch) {
		SequenceBatch &read_batch, SequenceBatch &barcode_batch) {
		double real_start_time = GetRealTime();
		uint32_t num_loaded_reads = 0;
		while (num_loaded_reads < read_batch_size_) {
		bool no_more_read = read_batch->LoadOneSequenceAndSaveAt(num_loaded_reads);
		bool no_more_read = read_batch.LoadOneSequenceAndSaveAt(num_loaded_reads);
		bool no_more_barcode = no_more_read;
		if (!is_bulk_data_) {
		no_more_barcode =
		barcode_batch->LoadOneSequenceAndSaveAt(num_loaded_reads);
		barcode_batch.LoadOneSequenceAndSaveAt(num_loaded_reads);
		}
		if ((!no_more_read) && (!no_more_barcode)) {
		if (read_batch->GetSequenceLengthAt(num_loaded_reads) <
		if (read_batch.GetSequenceLengthAt(num_loaded_reads) <
		(uint32_t)min_read_length_) {
		continue; // reads are too short, just drop.
		}

src/chromap.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -141,8 +141,8 @@ class Chromap {
		private:
		uint32_t SampleInputBarcodesAndExamineLength();

		uint32_t LoadSingleEndReadsWithBarcodes(SequenceBatch *read_batch,
		SequenceBatch *barcode_batch);
		uint32_t LoadSingleEndReadsWithBarcodes(SequenceBatch &read_batch,
		SequenceBatch &barcode_batch);

		uint32_t LoadPairedEndReadsWithBarcodes(SequenceBatch &read_batch1,
		SequenceBatch &read_batch2,

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