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#include <fstream>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/std/filesystem>
struct write_file_dummy_struct
{
std::filesystem::path const tmp_path = std::filesystem::temp_directory_path();
write_file_dummy_struct()
{
auto file_raw = R"////![fastq_file]";
std::ofstream file{tmp_path/"my.fastq"};
std::string str{file_raw};
file << str.substr(1); // skip first newline
}
~write_file_dummy_struct()
{
std::error_code ec{};
std::filesystem::path file_path{};
file_path = tmp_path/"my.fastq";
std::filesystem::remove(file_path, ec);
if (ec)
seqan3::debug_stream << "[WARNING] Could not delete " << file_path << ". " << ec.message() << '\n';
file_path = tmp_path/"output.fastq";
std::filesystem::remove(file_path, ec);
if (ec)
seqan3::debug_stream << "[WARNING] Could not delete " << file_path << ". " << ec.message() << '\n';
}
};
write_file_dummy_struct go{};
//![solution]
#include <seqan3/io/sequence_file/all.hpp>
#include <seqan3/range/views/persist.hpp>
#include <seqan3/std/filesystem>
#include <seqan3/std/ranges>
int main()
{
#if !SEQAN3_WORKAROUND_GCC_93983
std::filesystem::path tmp_dir = std::filesystem::temp_directory_path(); // get the temp directory
seqan3::sequence_file_input fin{tmp_dir/"my.fastq"};
seqan3::sequence_file_output fout{tmp_dir/"output.fastq"};
auto length_filter = std::views::filter([] (auto & rec)
{
return std::ranges::size(seqan3::get<seqan3::field::seq>(rec)) >= 5;
});
fout = fin | length_filter;
// This would also work:
// fin | length_filter | fout;
#endif // !SEQAN3_WORKAROUND_GCC_93983
}
//![solution]
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