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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <seqan3/core/platform.hpp>
#if SEQAN3_HAS_CEREAL
//![complete]
# include <fstream>
# include <seqan3/argument_parser/all.hpp>
# include <seqan3/io/sequence_file/input.hpp>
# include <seqan3/search/fm_index/bi_fm_index.hpp>
# include <cereal/archives/binary.hpp>
struct reference_storage_t
{
std::vector<std::string> ids;
std::vector<std::vector<seqan3::dna5>> seqs;
};
//! [solution]
void read_reference(std::filesystem::path const & reference_path, reference_storage_t & storage)
{
seqan3::sequence_file_input reference_in{reference_path};
for (auto && record : reference_in)
{
storage.ids.push_back(record.id());
storage.seqs.push_back(record.sequence());
}
}
//! [create_index]
void create_index(std::filesystem::path const & index_path, reference_storage_t & storage)
//! [create_index]
{
seqan3::bi_fm_index index{storage.seqs};
{
std::ofstream os{index_path, std::ios::binary};
cereal::BinaryOutputArchive oarchive{os};
oarchive(index);
}
}
void run_program(std::filesystem::path const & reference_path, std::filesystem::path const & index_path)
{
reference_storage_t storage{};
read_reference(reference_path, storage);
create_index(index_path, storage);
}
//! [solution]
struct cmd_arguments
{
std::filesystem::path reference_path{};
std::filesystem::path index_path{"out.index"};
};
void initialise_argument_parser(seqan3::argument_parser & parser, cmd_arguments & args)
{
parser.info.author = "E. coli";
parser.info.short_description = "Creates an index over a reference.";
parser.info.version = "1.0.0";
parser.add_option(args.reference_path,
'r',
"reference",
"The path to the reference.",
seqan3::option_spec::required,
seqan3::input_file_validator{{"fa", "fasta"}});
parser.add_option(args.index_path,
'o',
"output",
"The output index file path.",
seqan3::option_spec::standard,
seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"index"}});
}
int main(int argc, char const ** argv)
{
seqan3::argument_parser parser("Indexer", argc, argv);
cmd_arguments args{};
initialise_argument_parser(parser, args);
try
{
parser.parse();
}
catch (seqan3::argument_parser_error const & ext)
{
std::cerr << "[PARSER ERROR] " << ext.what() << '\n';
return -1;
}
run_program(args.reference_path, args.index_path);
return 0;
}
//![complete]
#endif //SEQAN3_HAS_CEREAL
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