Rename sequence effective range variables. (de54d9b2) · Commits · github_fork / Chromap

src/chromap.cc

+11 −11

Original line number	Diff line number	Diff line
		@@ -301,7 +301,7 @@ uint32_t Chromap::SampleInputBarcodesAndExamineLength() {
		uint32_t sample_batch_size = 1000;
		SequenceBatch barcode_batch(sample_batch_size);

		barcode_batch.SetSeqEffectiveRange(barcode_format_);
		barcode_batch.SetSeqEffectiveRange(barcode_effective_range_);

		barcode_batch.InitializeLoading(mapping_parameters_.barcode_file_paths[0]);

		@@ -382,7 +382,7 @@ void Chromap::LoadBarcodeWhitelist() {
		void Chromap::ComputeBarcodeAbundance(uint64_t max_num_sample_barcodes) {
		double real_start_time = GetRealTime();
		SequenceBatch barcode_batch(read_batch_size_);
		barcode_batch.SetSeqEffectiveRange(barcode_format_);
		barcode_batch.SetSeqEffectiveRange(barcode_effective_range_);
		for (size_t read_file_index = 0;
		read_file_index < mapping_parameters_.read_file1_paths.size();
		++read_file_index) {
		@@ -715,22 +715,22 @@ void Chromap::OutputMappingStatistics() {

		void Chromap::ParseReadFormat(const std::string &read_format) {
		uint32_t i, j;
		read1_format_.Init();
		read2_format_.Init();
		barcode_format_.Init();
		read1_effective_range_.Init();
		read2_effective_range_.Init();
		barcode_effective_range_.Init();
		for (i = 0; i < read_format.size();) {
		for (j = i + 1; j < read_format.size() && j != ','; ++j)
		;
		bool parse_success = true;
		if (read_format[i] == 'r' && read_format[i + 1] == '1') {
		parse_success =
		read1_format_.ParseEffectiveRange(read_format.c_str() + i, j - i);
		parse_success = read1_effective_range_.ParseEffectiveRange(
		read_format.c_str() + i, j - i);
		} else if (read_format[i] == 'r' && read_format[i + 1] == '2') {
		parse_success =
		read2_format_.ParseEffectiveRange(read_format.c_str() + i, j - i);
		parse_success = read2_effective_range_.ParseEffectiveRange(
		read_format.c_str() + i, j - i);
		} else if (read_format[i] == 'b' && read_format[i + 1] == 'c') {
		parse_success =
		barcode_format_.ParseEffectiveRange(read_format.c_str() + i, j - i);
		parse_success = barcode_effective_range_.ParseEffectiveRange(
		read_format.c_str() + i, j - i);
		} else {
		parse_success = false;
		}

src/chromap.h

+13 −13

Original line number	Diff line number	Diff line
		@@ -132,9 +132,9 @@ class Chromap {
		const uint32_t read_batch_size_ = 500000;

		// 0-start, 1-end (includsive), 2-strand(-1:minus, 1:plus)
		SequenceEffectiveRange barcode_format_;
		SequenceEffectiveRange read1_format_;
		SequenceEffectiveRange read2_format_;
		SequenceEffectiveRange barcode_effective_range_;
		SequenceEffectiveRange read1_effective_range_;
		SequenceEffectiveRange read2_effective_range_;

		std::vector<int> custom_rid_rank_;
		std::vector<int> pairs_custom_rid_rank_;
		@@ -188,10 +188,10 @@ void Chromap::MapSingleEndReads() {
		SequenceBatch read_batch_for_loading(read_batch_size_);
		SequenceBatch barcode_batch(read_batch_size_);
		SequenceBatch barcode_batch_for_loading(read_batch_size_);
		read_batch.SetSeqEffectiveRange(read1_format_);
		read_batch_for_loading.SetSeqEffectiveRange(read1_format_);
		barcode_batch.SetSeqEffectiveRange(barcode_format_);
		barcode_batch_for_loading.SetSeqEffectiveRange(barcode_format_);
		read_batch.SetSeqEffectiveRange(read1_effective_range_);
		read_batch_for_loading.SetSeqEffectiveRange(read1_effective_range_);
		barcode_batch.SetSeqEffectiveRange(barcode_effective_range_);
		barcode_batch_for_loading.SetSeqEffectiveRange(barcode_effective_range_);

		std::vector<std::vector<MappingRecord>> mappings_on_diff_ref_seqs;
		mappings_on_diff_ref_seqs.reserve(num_reference_sequences);
		@@ -559,12 +559,12 @@ void Chromap::MapPairedEndReads() {
		SequenceBatch read_batch2_for_loading(read_batch_size_);
		SequenceBatch barcode_batch_for_loading(read_batch_size_);

		read_batch1.SetSeqEffectiveRange(read1_format_);
		read_batch2.SetSeqEffectiveRange(read2_format_);
		barcode_batch.SetSeqEffectiveRange(barcode_format_);
		read_batch1_for_loading.SetSeqEffectiveRange(read1_format_);
		read_batch2_for_loading.SetSeqEffectiveRange(read2_format_);
		barcode_batch_for_loading.SetSeqEffectiveRange(barcode_format_);
		read_batch1.SetSeqEffectiveRange(read1_effective_range_);
		read_batch2.SetSeqEffectiveRange(read2_effective_range_);
		barcode_batch.SetSeqEffectiveRange(barcode_effective_range_);
		read_batch1_for_loading.SetSeqEffectiveRange(read1_effective_range_);
		read_batch2_for_loading.SetSeqEffectiveRange(read2_effective_range_);
		barcode_batch_for_loading.SetSeqEffectiveRange(barcode_effective_range_);

		// Initialize cache
		mm_cache mm_to_candidates_cache(2000003);

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