output in BED for single-cell data (59fb66ac) · Commits · github_fork / Chromap

src/output_tools.h

+30 −0

Original line number	Diff line number	Diff line
		@@ -126,11 +126,21 @@ class OutputTools {
		inline uint32_t GetNumMappings() const {
		return num_mappings_;
		}
		inline std::string Seed2Sequence(uint64_t seed, uint32_t seed_length) const {
		std::string sequence;
		sequence.reserve(seed_length);
		uint64_t mask = 3;
		for (uint32_t i = 0; i < seed_length; ++i) {
		sequence.push_back(SequenceBatch::Uint8ToChar((seed >> ((seed_length - 1 - i) * 2)) & mask));
		}
		return sequence;
		}

		protected:
		std::string mapping_output_file_path_;
		FILE *mapping_output_file_;
		uint32_t num_mappings_;
		uint32_t cell_barcode_length_ = 16;
		};

		template <typename MappingRecord>
		@@ -143,6 +153,16 @@ class BEDOutputTools : public OutputTools<MappingRecord> {
		}
		};

		template <>
		class BEDOutputTools<MappingWithBarcode> : public OutputTools<MappingWithBarcode> {
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingWithBarcode &mapping) {
		std::string strand = (mapping.mapq & 1) == 1 ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		uint32_t mapping_end_position = mapping.fragment_start_position + mapping.fragment_length;
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(mapping.fragment_start_position) + "\t" + std::to_string(mapping_end_position) + "\t" + Seed2Sequence(mapping.cell_barcode, cell_barcode_length_) +"\n");
		}
		};

		template <typename MappingRecord>
		class BEDPEOutputTools : public OutputTools<MappingRecord> {
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) {
		@@ -153,6 +173,16 @@ class BEDPEOutputTools : public OutputTools<MappingRecord> {
		}
		};

		template <>
		class BEDPEOutputTools<PairedEndMappingWithBarcode> : public OutputTools<PairedEndMappingWithBarcode> {
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const PairedEndMappingWithBarcode &mapping) {
		std::string strand = (mapping.mapq & 1) == 1 ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		uint32_t mapping_end_position = mapping.fragment_start_position + mapping.fragment_length;
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(mapping.fragment_start_position) + "\t" + std::to_string(mapping_end_position) + "\t" + Seed2Sequence(mapping.cell_barcode, cell_barcode_length_) + "\n");
		}
		};

		template <typename MappingRecord>
		class TagAlignOutputTools : public OutputTools<MappingRecord> {
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) {

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