seqan3::sam_file_input_options< sequence_legal_alphabet > Struct Template Reference

The options type defines various option members that influence the behaviour of all or some formats. More...

#include <seqan3/io/sam_file/input_options.hpp>

Inheritance diagram for seqan3::sam_file_input_options< sequence_legal_alphabet >:

Public Attributes
std::ostream *	stream_warnings_to {std::addressof(std::cerr)}
	The stream to write warnings to. Defaults to std::cerr.

Detailed Description

template<typename sequence_legal_alphabet>
struct seqan3::sam_file_input_options< sequence_legal_alphabet >

The options type defines various option members that influence the behaviour of all or some formats.

Remarks

For a complete overview, take a look at SAM File

Member Data Documentation

stream_warnings_to

template<typename sequence_legal_alphabet >

std::ostream* seqan3::sam_file_input_options< sequence_legal_alphabet >::stream_warnings_to {std::addressof(std::cerr)}

The stream to write warnings to. Defaults to std::cerr.

Example

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <sstream>
 
#include <seqan3/io/sam_file/input.hpp>
 
// A helper struct to create a temporary file and remove it when it goes out of scope.
struct temporary_file
{
    std::filesystem::path const path{std::filesystem::temp_directory_path() / "warnings.txt"};
 
    temporary_file()
    {
        std::ofstream file{path}; // Create file
    }
    temporary_file(temporary_file const &) = delete;
    temporary_file & operator=(temporary_file const &) = delete;
    temporary_file(temporary_file &&) = delete;
    temporary_file & operator=(temporary_file &&) = delete;
    ~temporary_file()
    {
        std::filesystem::remove(path);
    }
 
    std::string read_content() const
    {
        std::ifstream file{path};
        return std::string{std::istreambuf_iterator<char>{file}, std::istreambuf_iterator<char>{}};
    }
};
 
static constexpr auto sam_file_raw = R"(@HD VN:1.6  pb:5.0.0    ot:ter
@SQ SN:ref  LN:34
)";
 
static auto get_sam_file_input()
{
    return seqan3::sam_file_input{std::istringstream{sam_file_raw}, seqan3::format_sam{}};
}
 
void defaults_to_cerr()
{
    auto fin = get_sam_file_input();
    auto it = fin.begin();
}
 
void redirect_to_cout()
{
    auto fin = get_sam_file_input();
    fin.options.stream_warnings_to = std::addressof(std::cout); // Equivalent to `= &std::cout;`
    auto it = fin.begin();
}
 
void redirect_to_file()
{
    temporary_file tmp_file{};
    auto fin = get_sam_file_input();
 
    { // Inner scope to close file before reading
        std::ofstream warning_file{tmp_file.path};
        fin.options.stream_warnings_to = std::addressof(warning_file); // Equivalent to `= &warning_file;`
        auto it = fin.begin();
    }
 
    std::cout << "File content:\n" << tmp_file.read_content();
}
 
void silence_warnings()
{
    auto fin = get_sam_file_input();
    fin.options.stream_warnings_to = nullptr;
    auto it = fin.begin();
}
 
void filter()
{
    auto fin = get_sam_file_input();
    std::stringstream stream{};
    fin.options.stream_warnings_to = std::addressof(stream); // Equivalent to `= &stream;`
    auto it = fin.begin();
 
    for (std::string line{}; std::getline(stream, line);)
    {
        // If "pb" is not found in the warning, print it to cerr.
        if (line.find("pb") == std::string::npos) // C++23: `!line.contains("pb")`
            std::cerr << line << '\n';
    }
}
 
void print_section(std::string_view const section)
{
    std::cout << "### " << section << " ###\n";
    std::cerr << "### " << section << " ###\n";
}
 
int main()
{
    print_section("defaults_to_cerr");
    defaults_to_cerr();
 
    print_section("redirect_to_cout");
    redirect_to_cout();
 
    print_section("redirect_to_file");
    redirect_to_file();
 
    print_section("silence_warnings");
    silence_warnings();
 
    print_section("filter");
    filter();
}

Output to std::cerr:

### defaults_to_cerr ###
Unsupported tag found in SAM header @HD: "pb:5.0.0"
Unsupported tag found in SAM header @HD: "ot:ter"
### redirect_to_cout ###
### redirect_to_file ###
### silence_warnings ###
### filter ###
Unsupported tag found in SAM header @HD: "ot:ter"

Output to std::cout:

### defaults_to_cerr ###
### redirect_to_cout ###
Unsupported tag found in SAM header @HD: "pb:5.0.0"
Unsupported tag found in SAM header @HD: "ot:ter"
### redirect_to_file ###
File content:
Unsupported tag found in SAM header @HD: "pb:5.0.0"
Unsupported tag found in SAM header @HD: "ot:ter"
### silence_warnings ###
### filter ###

This entity is experimental and subject to change in the future. Experimental since version 3.4.

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The documentation for this struct was generated from the following file:

• sam_file/input_options.hpp