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#include <seqan3/argument_parser/all.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/io/sequence_file/input.hpp>
//! [solution]
//! [reference_storage_t]
struct reference_storage_t
{
std::vector<std::string> ids;
std::vector<std::vector<seqan3::dna5>> seqs;
};
//! [reference_storage_t]
//! [read_reference]
void read_reference(std::filesystem::path const & reference_path,
reference_storage_t & storage)
//! [read_reference]
{
seqan3::sequence_file_input reference_in{reference_path};
for (auto & [seq, id, qual] : reference_in)
{
storage.ids.push_back(std::move(id));
storage.seqs.push_back(std::move(seq));
}
seqan3::debug_stream << "Reference IDs: " << storage.ids << '\n';
}
void run_program(std::filesystem::path const & reference_path,
std::filesystem::path const & index_path)
{
seqan3::debug_stream << "reference_file_path: " << reference_path << '\n';
seqan3::debug_stream << "index_path " << index_path << '\n';
reference_storage_t storage{};
read_reference(reference_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::DEFAULT,
seqan3::output_file_validator{{"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;
}
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