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#include <fstream>
#include <iostream>
#include <terraces/advanced.hpp>
#include <terraces/parser.hpp>
#include <terraces/rooting.hpp>
#include <terraces/trees.hpp>
int main(int argc, char** argv) try {
if (argc != 3) {
std::cerr << "Usage: " << argv[0] << " <tree-file> <occurrence file>" << std::endl;
return 1;
}
auto data_file = std::ifstream{argv[2]};
const auto data = terraces::parse_bitmatrix(data_file);
auto tree_file = std::ifstream{argv[1]};
auto tree_string = std::string{};
std::getline(tree_file, tree_string);
auto tree = terraces::parse_nwk(tree_string, data.indices);
auto comp_taxon = terraces::find_comprehensive_taxon(data.matrix);
if (comp_taxon == terraces::none) {
std::cerr << "Cannot find a comprehensive taxon for the tree\n";
return 1;
}
terraces::reroot_at_taxon_inplace(tree, comp_taxon);
std::cout << as_newick(tree, data.names);
} catch (std::exception& e) {
std::cerr << "Error: " << e.what() << "\n";
}
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