fastq_writer.hpp

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#ifndef GENESIS_SEQUENCE_FORMATS_FASTQ_WRITER_H_
#define GENESIS_SEQUENCE_FORMATS_FASTQ_WRITER_H_

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2020 Lucas Czech

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/

#include "genesis/utils/io/output_target.hpp"

#include <iosfwd>
#include <string>

namespace genesis {
namespace sequence {

// =================================================================================================
//     Forward Declarations
// =================================================================================================

class Sequence;
class SequenceSet;

// =================================================================================================
//     Fastq Writer
// =================================================================================================

class FastqWriter
{
public:

    // ---------------------------------------------------------------------
    //     Constructor and Rule of Five
    // ---------------------------------------------------------------------

    FastqWriter()  = default;
    ~FastqWriter() = default;

    FastqWriter( FastqWriter const& ) = default;
    FastqWriter( FastqWriter&& )      = default;

    FastqWriter& operator= ( FastqWriter const& ) = default;
    FastqWriter& operator= ( FastqWriter&& )      = default;

    // ---------------------------------------------------------------------
    //     Writing
    // ---------------------------------------------------------------------

    void write( Sequence const& sequence, std::shared_ptr<utils::BaseOutputTarget> target ) const;

    void write( SequenceSet const& sequence_set, std::shared_ptr<utils::BaseOutputTarget> target ) const;

    void write_sequence( Sequence const& sequence, std::ostream& os ) const;

    // ---------------------------------------------------------------------
    //     Properties
    // ---------------------------------------------------------------------

    FastqWriter& line_length( size_t value );

    size_t line_length() const;

    FastqWriter& fill_missing_quality( unsigned char value );

    unsigned char fill_missing_quality() const;

    FastqWriter& repeat_label( bool value );

    bool repeat_label() const;

    // ---------------------------------------------------------------------
    //     Members
    // ---------------------------------------------------------------------

private:

    size_t line_length_ = 0;
    unsigned char fill_missing_quality_ = 255;
    bool repeat_label_ = false;

};

} // namespace sequence
} // namespace genesis

#endif // include guard