Merge branch 'li_dev' of https://github.com/haowenz/chromap into li_dev (93366593) · Commits · github_fork / Chromap

src/chromap.cc

+1 −0

Original line number	Diff line number	Diff line
		@@ -1531,6 +1531,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		output_tools_ = std::unique_ptr<SAMOutputTools<MappingRecord> >(new SAMOutputTools<MappingRecord>);
		}
		output_tools_->InitializeMappingOutput(mapping_output_file_path_);
		output_tools_->OutputHeader(num_reference_sequences, reference);
		mm_cache mm_to_candidates_cache(2000003);
		mm_to_candidates_cache.SetKmerLength(kmer_size_);
		struct _mm_history *mm_history = new struct _mm_history[read_batch_size_];

src/output_tools.h

+20 −0

Original line number	Diff line number	Diff line
		@@ -550,6 +550,7 @@ class OutputTools {
		inline void AppendMappingOutput(const std::string &line) {
		fprintf(mapping_output_file_, "%s", line.data());
		}
		virtual void OutputHeader(uint32_t num_reference_sequences, const SequenceBatch &reference) = 0;
		virtual void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) = 0;
		inline std::string GeneratePAFLine(const SequenceBatch &query_batch, uint32_t query_index, const int query_start, const int query_end, const char relative_strand, const SequenceBatch &target_batch, uint32_t target_index, const int target_start, const int target_end, const int num_matches, const int alignment_length, const int mapping_quality) {
		return std::string(query_batch.GetSequenceNameAt(query_index)) + "\t" + std::to_string(query_batch.GetSequenceLengthAt(query_index)) + "\t" + std::to_string(query_start) + "\t" + std::to_string(query_end) + "\t" + relative_strand + "\t" + std::string(target_batch.GetSequenceNameAt(target_index)) + "\t" + std::to_string(target_batch.GetSequenceLengthAt(target_index)) + "\t" + std::to_string(target_start) + "\t" + std::to_string(target_end) + "\t" + std::to_string(num_matches) + "\t" + std::to_string(alignment_length) + "\t" + std::to_string(mapping_quality) + "\n";
		@@ -617,6 +618,8 @@ class OutputTools {

		template <typename MappingRecord>
		class BEDOutputTools : public OutputTools<MappingRecord> {
		void OutputHeader(uint32_t num_reference_sequences, const SequenceBatch &reference) {
		}
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) {
		std::string strand = mapping.IsPositive() ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		@@ -635,6 +638,8 @@ inline void BEDOutputTools<MappingWithBarcode>::AppendMapping(uint32_t rid, cons

		template <typename MappingRecord>
		class BEDPEOutputTools : public OutputTools<MappingRecord> {
		void OutputHeader(uint32_t num_reference_sequences, const SequenceBatch &reference) {
		}
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) {
		std::string strand = mapping.IsPositive() ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		@@ -655,6 +660,8 @@ template <>

		template <typename MappingRecord>
		class TagAlignOutputTools : public OutputTools<MappingRecord> {
		void OutputHeader(uint32_t num_reference_sequences, const SequenceBatch &reference) {
		}
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) {
		std::string strand = mapping.IsPositive() ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		@@ -665,6 +672,8 @@ class TagAlignOutputTools : public OutputTools<MappingRecord> {

		template <typename MappingRecord>
		class PairedTagAlignOutputTools : public OutputTools<MappingRecord> {
		void OutputHeader(uint32_t num_reference_sequences, const SequenceBatch &reference) {
		}
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) {
		bool positive_strand = mapping.IsPositive();
		uint32_t positive_read_end = mapping.fragment_start_position + mapping.positive_alignment_length;
		@@ -685,6 +694,8 @@ inline void PairedTagAlignOutputTools<SAMMapping>::AppendMapping(uint32_t rid, c

		template <typename MappingRecord>
		class PAFOutputTools : public OutputTools<MappingRecord> {
		void OutputHeader(uint32_t num_reference_sequences, const SequenceBatch &reference) {
		}
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) {
		}
		};
		@@ -718,6 +729,8 @@ inline void PAFOutputTools<MappingWithoutBarcode>::AppendMapping(uint32_t rid, c

		template <typename MappingRecord>
		class PairedPAFOutputTools : public OutputTools<MappingRecord> {
		void OutputHeader(uint32_t num_reference_sequences, const SequenceBatch &reference) {
		}
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) {
		}
		};
		@@ -743,6 +756,13 @@ template <typename MappingRecord>
		class SAMOutputTools : public OutputTools<MappingRecord> {
		inline void AppendMapping(uint32_t rid, const SequenceBatch &reference, const MappingRecord &mapping) {
		}
		void OutputHeader(uint32_t num_reference_sequences, const SequenceBatch &reference) {
		for (uint32_t rid = 0; rid < num_reference_sequences; ++rid) {
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		uint32_t reference_sequence_length = reference.GetSequenceLengthAt(rid);
		this->AppendMappingOutput("@SQ\tSN:" + std::string(reference_sequence_name) + "\tLN:"+ std::to_string(reference_sequence_length) + "\n");
		}
		}
		};

		template <>

Admin message