Output mapq in BED format. Update readme (c427ed87) · Commits · github_fork / Chromap

README.md

+8 −1

Original line number	Diff line number	Diff line
		@@ -113,6 +113,13 @@ threshold to make a correction by setting --bc-probability-threshold
		corrections. For scATAC-seq data with multiple read and barcode files, you can
		use "," to concatenate multiple input files as the example [above](#general).

		The BED format (fragment file) for bulk and single-cell are different except for the first
		three columns. For bulk data, the columns are "chrom chrom_start chrom_end N mapq strand".
		For single-cell data, the columns are "chrom chrom_start chrom_end barcode duplicate_count"
		as the definition of the fragment file in
		[CellRanger](https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments).
		Note that chrom_end is open-end.

		#### <a name="map-hic"></a>Map Hi-C short reads

		```sh

src/output_tools.h

+5 −5

Original line number	Diff line number	Diff line
		@@ -1033,7 +1033,7 @@ class BEDOutputTools : public OutputTools<MappingRecord> {
		std::string strand = mapping.IsPositive() ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		uint32_t mapping_end_position = mapping.GetEndPosition();
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(mapping.GetStartPosition()) + "\t" + std::to_string(mapping_end_position) + "\tN\t1000\t" + strand + "\n");
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(mapping.GetStartPosition()) + "\t" + std::to_string(mapping_end_position) + "\tN\t" + std::to_string(mapping.mapq) + "\t" + strand + "\n");
		}
		};

		@@ -1053,7 +1053,7 @@ class BEDPEOutputTools : public OutputTools<MappingRecord> {
		std::string strand = mapping.IsPositive() ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		uint32_t mapping_end_position = mapping.GetEndPosition();
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(mapping.GetStartPosition()) + "\t" + std::to_string(mapping_end_position) + "\tN\t1000\t" + strand + "\n");
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(mapping.GetStartPosition()) + "\t" + std::to_string(mapping_end_position) + "\tN\t" + std::to_string(mapping.mapq) + "\t" + strand + "\n");
		}
		};

		@@ -1075,7 +1075,7 @@ class TagAlignOutputTools : public OutputTools<MappingRecord> {
		std::string strand = mapping.IsPositive() ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		uint32_t mapping_end_position = mapping.GetEndPosition();
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(mapping.GetStartPosition()) + "\t" + std::to_string(mapping_end_position) + "\tN\t1000\t" + strand + "\n");
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(mapping.GetStartPosition()) + "\t" + std::to_string(mapping_end_position) + "\tN\t" + std::to_string(mapping.mapq) + "\t" + strand + "\n");
		}
		};

		@@ -1090,9 +1090,9 @@ class PairedTagAlignOutputTools : public OutputTools<MappingRecord> {
		uint32_t negative_read_start = negative_read_end - mapping.negative_alignment_length;
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		if (positive_strand) {
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(mapping.fragment_start_position) + "\t" + std::to_string(positive_read_end) + "\tN\t1000\t+\n" + std::string(reference_sequence_name) + "\t" + std::to_string(negative_read_start) + "\t" + std::to_string(negative_read_end) + "\tN\t1000\t-\n");
		this->AppendMappingOutput(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::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");
		} else {
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" + std::to_string(negative_read_start) + "\t" + std::to_string(negative_read_end) + "\tN\t1000\t-\n" + std::string(reference_sequence_name) + "\t" + std::to_string(mapping.fragment_start_position) + "\t" + std::to_string(positive_read_end) + "\tN\t1000\t+\n");
		this->AppendMappingOutput(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::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");
		}
		}
		};

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