// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2019, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2019, 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/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------

/*!\file
 * \brief Provides seqan3::alignment_file_output_options.
 * \author Svenja Mehringer <svenja.mehringer AT fu-berlin.de>
 */

#pragma once

#include <seqan3/core/platform.hpp>

namespace seqan3
{

//!\brief The options type defines various option members that influence the behavior of all or some formats.
//!\ingroup alignment_file
struct alignment_file_output_options
{
    /*!\brief The default plain text line-ending is "\n", but on Windows an
     *        additional carriage return is recommended ("\r\n" for line-ending).
     */
    bool add_carriage_return = false;

    /*!\brief Whether to require a header for SAM files.
     *
     * \details
     *
     * In the official SAM format the header is optional but we highly
     * recommend to always specify the header nonetheless to be consistent with
     * BAM files (where the header is always required).
     * If you explicitly want the header not to be written and no related
     * checks to be done (e.g. the record reference name must be present in
     * the reference dictionary of the header) you may set this variable to
     * `false`.
     */
    bool sam_require_header = true;
};

} // namespace seqan3
