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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/test/snippet/create_temporary_snippet_file.hpp>
// std::filesystem::current_path() / "out.sam" will be deleted after the execution
seqan3::test::create_temporary_snippet_file example_sam{"out.sam", ""};
//![main]
#include <seqan3/io/sam_file/all.hpp>
int main()
{
using namespace seqan3::literals;
auto filename = std::filesystem::current_path() / "out.sam";
seqan3::sam_file_output fout{filename};
using types = seqan3::type_list<std::vector<seqan3::dna5>, std::string, std::vector<seqan3::cigar>>;
using fields = seqan3::fields<seqan3::field::seq, seqan3::field::id, seqan3::field::cigar>;
using sam_record_type = seqan3::sam_record<types, fields>;
// write the following to the file
// r001 0 * 0 0 4M2I2M2D * 0 0 ACGTACGT *
sam_record_type record{};
record.id() = "r001";
record.sequence() = "ACGTACGT"_dna5;
record.cigar_sequence() = {{4, 'M'_cigar_operation},
{2, 'I'_cigar_operation},
{2, 'M'_cigar_operation},
{2, 'D'_cigar_operation}};
fout.push_back(record);
}
//![main]
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