Output duplication number in bulk bed format too. (16792ede) · Commits · github_fork / Chromap

src/bed_mapping.h

+3 −3

Original line number	Diff line number	Diff line
		@@ -68,11 +68,11 @@ class MappingWithoutBarcode : public Mapping {
		uint16_t fragment_length_;
		// uint8_t mapq;
		uint8_t mapq_ : 6, direction_ : 1, is_unique_ : 1;
		uint8_t num_dups_;
		uint16_t num_dups_; // Need higher limit in bulk setting

		MappingWithoutBarcode() : num_dups_(0) {}
		MappingWithoutBarcode(uint32_t read_id, uint32_t fragment_start_position,
		uint16_t fragment_length, uint8_t mapq,
		uint16_t fragment_length, uint16_t mapq,
		uint8_t direction, uint8_t is_unique, uint8_t num_dups)
		: read_id_(read_id),
		fragment_start_position_(fragment_start_position),
		@@ -192,7 +192,7 @@ class PairedEndMappingWithoutBarcode : public Mapping {
		uint32_t fragment_start_position,
		uint16_t fragment_length, uint8_t mapq,
		uint8_t direction, uint8_t is_unique,
		uint8_t num_dups,
		uint16_t num_dups,
		uint16_t positive_alignment_length,
		uint16_t negative_alignment_length)
		: read_id_(read_id),

src/mapping_writer.cc

+7 −5

Original line number	Diff line number	Diff line
		@@ -50,7 +50,7 @@ void MappingWriter<MappingWithoutBarcode>::AppendMapping(
		std::to_string(mapping.GetStartPosition()) +
		"\t" + std::to_string(mapping_end_position) +
		"\tN\t" + std::to_string(mapping.mapq_) + "\t" +
		strand + "\n");
		strand + "\t" + std::to_string(mapping.num_dups_) + "\n");
		} else {
		std::string strand = mapping.IsPositiveStrand() ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		@@ -59,7 +59,7 @@ void MappingWriter<MappingWithoutBarcode>::AppendMapping(
		std::to_string(mapping.GetStartPosition()) +
		"\t" + std::to_string(mapping_end_position) +
		"\tN\t" + std::to_string(mapping.mapq_) + "\t" +
		strand + "\n");
		strand + "\t" + std::to_string(mapping.num_dups_) + "\n");
		}
		}

		@@ -80,7 +80,7 @@ void MappingWriter<PairedEndMappingWithoutBarcode>::AppendMapping(
		std::to_string(mapping.GetStartPosition()) +
		"\t" + std::to_string(mapping_end_position) +
		"\tN\t" + std::to_string(mapping.mapq_) + "\t" +
		strand + "\n");
		strand + "\t" + std::to_string(mapping.num_dups_) + "\n");
		} else {
		bool positive_strand = mapping.IsPositiveStrand();
		uint32_t positive_read_end =
		@@ -99,7 +99,8 @@ void MappingWriter<PairedEndMappingWithoutBarcode>::AppendMapping(
		std::string(reference_sequence_name) + "\t" +
		std::to_string(negative_read_start) + "\t" +
		std::to_string(negative_read_end) + "\tN\t" +
		std::to_string(mapping.mapq_) + "\t-\n");
		std::to_string(mapping.mapq_) + "\t-\t" +
		std::to_string(mapping.num_dups_) + "\n");
		} else {
		this->AppendMappingOutput(
		std::string(reference_sequence_name) + "\t" +
		@@ -109,7 +110,8 @@ void MappingWriter<PairedEndMappingWithoutBarcode>::AppendMapping(
		std::string(reference_sequence_name) + "\t" +
		std::to_string(mapping.fragment_start_position_) + "\t" +
		std::to_string(positive_read_end) + "\tN\t" +
		std::to_string(mapping.mapq_) + "\t+\n");
		std::to_string(mapping.mapq_) + "\t+\t" +
		std::to_string(mapping.num_dups_) + "\n");
		}
		}
		}

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