I/O API design - Hannes vs. Current

ex1.cpp

// Standard example
===================

// current implementation:
seqan3::sequence_file_input in{"x.fasta"};

for (auto && rec : in)
    seqan3::debug_stream << rec.sequence();

// -------------------------------------------------------------------------------------------------------------------------

// Hannes implementation:
seqan3::seq_io::reader in{"x.fasta"};

for (auto && rec : in)
    seqan3::debug_stream << rec.sequence();

ex2.cpp

// Decomposition example
========================

// current implementation:
seqan3::sequence_file_input in{"x.fasta"};

for (auto & [ i, s, q ] : in)
    seqan3::debug_stream << "ID:  " << i << '\n';

// -------------------------------------------------------------------------------------------------------------------------

// Hannes implementation:
seqan3::seq_io::reader reader{"example.fasta"};

for (auto & [ i, s, q ] : reader)
    seqan3::debug_stream << "ID:  " << i << '\n';

ex3.cpp

// Simple options example
=========================

// current implementation:
seqan3::sequence_file_input in{"x.fasta"};
in.options.truncate_ids = true; // must (should?) be done before the first record is read

// -------------------------------------------------------------------------------------------------------------------------

// Hannes implementation:
seqan3::seq_io::reader reader{"example.fasta", seqan3::seq_io::reader_options{.truncate_ids = true }};

ex4.cpp

// Select different types
=========================

// current implementation:
struct my_traits : seqan3::sequence_file_input_default_traits_dna
{
    using sequence_alphabet = char; // instead of dna5
 
    template <typename alph>
    using sequence_container = std::basic_string<alph>; // must be defined as a template! String_view is not possible
};

seqan3::sequence_file_input<my_traits> fin{"x.fasta"};

// -------------------------------------------------------------------------------------------------------------------------

// Hannes implementation:
seqan3::seq_io::reader reader{"example.fasta",
                              seqan3::seq_io::reader_options{
                                    .field_types = seqan3::ttag<std::string_view, std::string, std::string>};

ex5.cpp

// Select different fields
=========================

// current implementation:
seqan3::sequence_file_input fin{"x.fasta", seqan3::fields<seqan3::field::id, seqan3::field::qual>()};

// -------------------------------------------------------------------------------------------------------------------------

// Hannes implementation:
seqan3::seq_io::reader reader{"example.fasta",
                              seqan3::seq_io::reader_options{
                                    .field_ids   = bio::vtag<seqan3::field::id, seqan3::field::qual>,
                                    .field_types = seqan3::ttag<std::string_view, std::vector<seqan3::phred62>>}; // tyoes have to be also given