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#include <fstream>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/std/filesystem>
struct write_file_dummy_struct
{
std::filesystem::path const file_path = std::filesystem::temp_directory_path()/"example.sam";
write_file_dummy_struct()
{
auto file_raw = R"////![sam_file]";
std::ofstream file{file_path};
std::string str{file_raw};
file << str.substr(1); // skip first newline
}
~write_file_dummy_struct()
{
std::error_code ec{};
std::filesystem::remove(file_path, ec);
if (ec)
seqan3::debug_stream << "[WARNING] Could not delete " << file_path << ". " << ec.message() << '\n';
}
};
write_file_dummy_struct go{};
//![main]
#include <seqan3/io/alignment_file/all.hpp>
int main()
{
//![main]
{
//![writing]
auto filename = std::filesystem::temp_directory_path()/"out.sam";
seqan3::alignment_file_output fout{filename, seqan3::fields<seqan3::field::flag, seqan3::field::mapq>{}};
size_t mymapq{0};
seqan3::sam_flag flag{seqan3::sam_flag::unmapped};
// ...
fout.emplace_back(flag, mymapq);
// or:
fout.push_back(std::tie(flag, mymapq));
//![writing]
}
{
//![file_extensions]
seqan3::debug_stream << seqan3::format_sam::file_extensions << '\n'; // prints [fastq,fq]
seqan3::format_sam::file_extensions.push_back("sm");
//![file_extensions]
}
{
/*
//![filename_construction]
seqan3::alignment_file_input fin_from_filename{"/tmp/my.sam"};
seqan3::alignment_file_input fin_from_stream{std::cin, seqan3::format_sam{}};
//![filename_construction]
*/
}
{
//![read_custom_fields]
auto filename = std::filesystem::temp_directory_path()/"example.sam";
seqan3::alignment_file_input fin{filename, seqan3::fields<seqan3::field::id,
seqan3::field::seq,
seqan3::field::flag>{}};
for (auto & [id, seq, flag /*order!*/] : fin)
{
seqan3::debug_stream << id << '\n';
seqan3::debug_stream << seq << '\n';
seqan3::debug_stream << flag << '\n';
}
//![read_custom_fields]
}
{
//![alignments_without_ref]
auto filename = std::filesystem::temp_directory_path()/"example.sam";
seqan3::alignment_file_input fin{filename, seqan3::fields<seqan3::field::id, seqan3::field::alignment>{}};
for (auto & [ id, alignment ] : fin)
{
seqan3::debug_stream << id << ": " << std::get<1>(alignment) << '\n';
}
//![alignments_without_ref]
}
{
//![alignments_with_ref]
using seqan3::operator""_dna5;
auto filename = std::filesystem::temp_directory_path()/"example.sam";
std::vector<std::string> ref_ids{"ref"}; // list of one reference name
std::vector<seqan3::dna5_vector> ref_sequences{"AGAGTTCGAGATCGAGGACTAGCGACGAGGCAGCGAGCGATCGAT"_dna5};
seqan3::alignment_file_input fin{filename, ref_ids, ref_sequences, seqan3::fields<seqan3::field::alignment>{}};
for (auto & [ alignment ] : fin)
{
seqan3::debug_stream << alignment << '\n'; // Now you can print the whole alignment!
}
//![alignments_with_ref]
}
std::filesystem::remove(std::filesystem::temp_directory_path()/"out.sam");
//![main_end]
}
//![main_end]
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