Rename the variable to avoid confusion. (17abb1bd) · Commits · github_fork / Chromap

chromap.1

+1 −1

Original line number	Diff line number	Diff line
		.TH chromap 1 "22 Feb 2022" "chromap-0.2 (r353)" "Bioinformatics tools"
		.TH chromap 1 "22 Feb 2022" "chromap-0.2 (r354)" "Bioinformatics tools"
		.SH NAME
		.PP
		chromap - fast alignment and preprocessing of chromatin profiles

+1 −1

+1 −1

Original line number	Diff line number	Diff line
		@@ -378,7 +378,7 @@ void MappingWriter<PairsMapping>::OutputHeader(uint32_t num_reference_sequences,
		rid_order.resize(num_reference_sequences);
		uint32_t i;
		for (i = 0; i < num_reference_sequences; ++i) {
		rid_order[custom_rid_rank_[i]] = i;
		rid_order[pairs_custom_rid_rank_[i]] = i;
		}
		this->AppendMappingOutput("## pairs format v1.0.0\n#shape: upper triangle\n");
		for (i = 0; i < num_reference_sequences; ++i) {

+3 −3

Original line number	Diff line number	Diff line
		@@ -31,10 +31,10 @@ class MappingWriter {

		MappingWriter(const MappingParameters mapping_parameters,
		const uint32_t cell_barcode_length,
		const std::vector<int> &custom_rid_rank)
		const std::vector<int> &pairs_custom_rid_rank)
		: mapping_parameters_(mapping_parameters),
		cell_barcode_length_(cell_barcode_length),
		custom_rid_rank_(custom_rid_rank) {
		pairs_custom_rid_rank_(pairs_custom_rid_rank) {
		if (!mapping_parameters_.barcode_translate_table_file_path.empty()) {
		barcode_translator_.SetTranslateTable(
		mapping_parameters_.barcode_translate_table_file_path);
		@@ -111,7 +111,7 @@ class MappingWriter {
		FILE *mapping_output_file_ = nullptr;
		BarcodeTranslator barcode_translator_;
		// for pairs
		const std::vector<int> custom_rid_rank_;
		const std::vector<int> pairs_custom_rid_rank_;
		};

		template <typename MappingRecord>