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raptor.cpp
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raptor.cpp
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// --------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2022, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
// --------------------------------------------------------------------------------------------------
#include <raptor/argument_parsing/build_parsing.hpp>
#include <raptor/argument_parsing/init_shared_meta.hpp>
#include <raptor/argument_parsing/search_parsing.hpp>
#include <raptor/argument_parsing/upgrade_parsing.hpp>
#include <raptor/raptor.hpp>
int main(int argc, char ** argv)
{
try
{
sharg::parser top_level_parser{"raptor",
argc,
argv,
sharg::update_notifications::on,
{"build", "search", "socks", "upgrade"}};
raptor::init_shared_meta(top_level_parser);
top_level_parser.info.description.emplace_back(
"Raptor is a system for approximately searching many queries such as "
"next-generation sequencing reads or transcripts in large collections of "
"nucleotide sequences. Raptor uses winnowing minimizers to define a set of "
"representative k-mers, an extension of the interleaved Bloom filters (IBFs) "
"as a set membership data structure and probabilistic thresholding for "
"minimizers. Our approach allows compression and partitioning of the IBF to "
"enable the effective use of secondary memory.");
top_level_parser.parse();
sharg::parser & sub_parser = top_level_parser.get_sub_parser();
if (sub_parser.info.app_name == std::string_view{"raptor-build"})
raptor::build_parsing(sub_parser, false);
if (sub_parser.info.app_name == std::string_view{"raptor-search"})
raptor::search_parsing(sub_parser, false);
if (sub_parser.info.app_name == std::string_view{"raptor-socks"})
{
sharg::parser socks_parser{"socks",
argc - 1,
argv + 1,
sharg::update_notifications::off,
{"build", "lookup-kmer"}};
socks_parser.parse();
sharg::parser & socks_sub_parser = socks_parser.get_sub_parser();
if (socks_sub_parser.info.app_name == std::string_view{"socks-build"})
raptor::build_parsing(socks_sub_parser, true);
if (socks_sub_parser.info.app_name == std::string_view{"socks-lookup-kmer"})
raptor::search_parsing(socks_sub_parser, true);
}
if (sub_parser.info.app_name == std::string_view{"raptor-upgrade"})
raptor::upgrade_parsing(sub_parser);
}
catch (sharg::parser_error const & ext)
{
std::cerr << "[Error] " << ext.what() << '\n';
std::exit(-1);
}
return 0;
}