Change fragment order in output (e42cd8e2) · Commits · github_fork / Chromap

src/chromap.cc

+3 −3

Original line number	Diff line number	Diff line
		@@ -760,6 +760,9 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		delete[] mm_history1;
		delete[] mm_history2;
		OutputMappingStatistics();
		if (!is_bulk_data_) {
		OutputBarcodeStatistics();
		}
		index.Destroy();
		if (low_memory_mode_) {
		if (num_mappings_in_mem > 0) {
		@@ -856,9 +859,6 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		// Delete temp files
		} else {
		OutputMappingStatistics(num_reference_sequences, mappings_on_diff_ref_seqs_, mappings_on_diff_ref_seqs_);
		if (!is_bulk_data_) {
		OutputBarcodeStatistics();
		}
		if (Tn5_shift_) {
		ApplyTn5ShiftOnPairedEndMapping(num_reference_sequences, &mappings_on_diff_ref_seqs_);
		}

src/output_tools.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -63,7 +63,7 @@ struct MappingWithBarcode {
		uint8_t num_dups;
		//uint8_t mapq;
		bool operator<(const MappingWithBarcode& m) const {
		return std::tie(cell_barcode, fragment_start_position, fragment_length, mapq, direction, is_unique, read_id) < std::tie(m.cell_barcode, m.fragment_start_position, m.fragment_length, m.mapq, m.direction, m.is_unique, m.read_id);
		return std::tie(fragment_start_position, fragment_length, cell_barcode, mapq, direction, is_unique, read_id) < std::tie(m.fragment_start_position, m.fragment_length, m.cell_barcode, m.mapq, m.direction, m.is_unique, m.read_id);
		}
		bool operator==(const MappingWithBarcode& m) const {
		return std::tie(cell_barcode, fragment_start_position) == std::tie(m.cell_barcode, m.fragment_start_position);
		@@ -96,7 +96,7 @@ struct PairedEndMappingWithBarcode {
		uint16_t positive_alignment_length;
		uint16_t negative_alignment_length;
		bool operator<(const PairedEndMappingWithBarcode& m) const {
		return std::tie(cell_barcode, fragment_start_position, fragment_length, mapq, direction, is_unique, read_id, positive_alignment_length, negative_alignment_length) < std::tie(m.cell_barcode, m.fragment_start_position, m.fragment_length, m.mapq, m.direction, m.is_unique, m.read_id, m.positive_alignment_length, m.negative_alignment_length);
		return std::tie(fragment_start_position, fragment_length, cell_barcode, mapq, direction, is_unique, read_id, positive_alignment_length, negative_alignment_length) < std::tie(m.fragment_start_position, m.fragment_length, m.cell_barcode, m.mapq, m.direction, m.is_unique, m.read_id, m.positive_alignment_length, m.negative_alignment_length);
		}
		bool operator==(const PairedEndMappingWithBarcode& m) const {
		return std::tie(cell_barcode, fragment_start_position, fragment_length) == std::tie(m.cell_barcode, m.fragment_start_position, m.fragment_length);

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