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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/argument_parser/all.hpp>
#include <seqan3/core/debug_stream.hpp>
void run_program(std::filesystem::path const & reference_path,
std::filesystem::path const & query_path,
std::filesystem::path const & index_path,
std::filesystem::path const & sam_path,
uint8_t const errors)
{
seqan3::debug_stream << "reference_path: " << reference_path << '\n';
seqan3::debug_stream << "query_path: " << query_path << '\n';
seqan3::debug_stream << "index_path " << index_path << '\n';
seqan3::debug_stream << "sam_path " << sam_path << '\n';
seqan3::debug_stream << "errors: " << errors << '\n';
}
struct cmd_arguments
{
std::filesystem::path reference_path{};
std::filesystem::path query_path{};
std::filesystem::path index_path{};
std::filesystem::path sam_path{"out.sam"};
uint8_t errors{0};
};
void initialise_argument_parser(seqan3::argument_parser & parser, cmd_arguments & args)
{
parser.info.author = "E. coli";
parser.info.short_description = "Map reads against 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.query_path,
'q',
"query",
"The path to the query.",
seqan3::option_spec::required,
seqan3::input_file_validator{{"fq", "fastq"}});
parser.add_option(args.index_path,
'i',
"index",
"The path to the index.",
seqan3::option_spec::required,
seqan3::input_file_validator{{"index"}});
parser.add_option(args.sam_path,
'o',
"output",
"The output SAM file path.",
seqan3::option_spec::standard,
seqan3::output_file_validator{seqan3::output_file_open_options::create_new, {"sam"}});
parser.add_option(args.errors,
'e',
"error",
"Maximum allowed errors.",
seqan3::option_spec::standard,
seqan3::arithmetic_range_validator{0, 4});
}
//![main]
int main(int argc, char const ** argv)
{
seqan3::argument_parser parser("Mapper", 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.query_path, args.index_path, args.sam_path, args.errors);
return 0;
}
//![main]
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