//! [read]
#include <string>                            // for std::string
#include <vector>                            // for std::vector
#include <seqan3/argument_parser/all.hpp>    // for argument_parser
#include <seqan3/core/debug_stream.hpp>      // for debug_stream
#include <seqan3/io/sequence_file/input.hpp> // for sequence_file_input

int main(int argc, char * argv[])
{
    // Receive the filename as program argument.
    std::string filename{};
    seqan3::argument_parser parser("My-first-program", argc, argv);
    parser.add_positional_option(filename, "The filename of the file to read.");
    try
    {
        parser.parse();
    }
    catch (seqan3::parser_invalid_argument const & ext)
    {
        seqan3::debug_stream << "[PARSER ERROR] " << ext.what() << '\n';
        return 0;
    }
    seqan3::debug_stream << "Reading file " << filename << "\n";

    // Create the vector to store sequences of type seqan3::dna5_vector.
    std::vector<seqan3::dna5_vector> sequences;

    // Iterate through the file and store the sequences.
    seqan3::sequence_file_input file_in{filename};
    for (auto & [ seq, id, qual ] : file_in)
    {
        sequences.push_back(seq);
    }
}
//! [read]
