A toolkit for working with phylogenetic data.
v0.20.0
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ncbi.cpp File Reference
#include "genesis/taxonomy/formats/ncbi.hpp"
#include <cassert>
#include <fstream>
#include <functional>
#include <stdexcept>
#include <vector>

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Namespaces

 genesis
 Container namespace for all symbols of genesis in order to keep them separate when used as a library.
 
 genesis::taxonomy
 

Functions

NcbiNameLookup convert_ncbi_name_table (utils::CsvReader::Table const &name_table, size_t tax_id_pos, size_t name_pos, size_t name_class_pos, std::string name_class_filter)
 
NcbiNodeLookup convert_ncbi_node_table (utils::CsvReader::Table const &node_table, size_t tax_id_pos, size_t parent_tax_id_pos, size_t rank_pos)
 
Taxonomy convert_ncbi_tables (NcbiNodeLookup const &nodes, NcbiNameLookup const &names)
 
Taxonomy read_ncbi_taxonomy (std::string const &node_file, std::string const &name_file)