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) 2014-2024 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@sund.ku.dk>
    University of Copenhagen, Globe Institute, Section for GeoGenetics
    Oster Voldgade 5-7, 1350 Copenhagen K, Denmark
*/
 
#include "genesis/utils/io/output_target.hpp"
 
#include <iosfwd>
#include <string>
 
#if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
 
    #include <string_view>
 
#endif
 
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(
        Sequence const& sequence,
        std::string const& quality,
        std::shared_ptr<utils::BaseOutputTarget> target
    ) const;
 
    void write(
        SequenceSet const& sequence_set,
        std::shared_ptr<utils::BaseOutputTarget> target
    ) const;
 
    #if ((defined(_MSVC_LANG) && _MSVC_LANG >= 201703L) || __cplusplus >= 201703L)
 
    void write(
        std::string_view const& label,
        std::string_view const& sites,
        std::string_view const& quality,
        std::shared_ptr<utils::BaseOutputTarget> target
    ) const;
 
    #endif
 
    // ---------------------------------------------------------------------
    //     Properties
    // ---------------------------------------------------------------------
 
    FastqWriter& line_length( size_t value )
    {
        line_length_ = value;
        return *this;
    }
 
    size_t line_length() const
    {
        return line_length_;
    }
 
    FastqWriter& fill_missing_quality( unsigned char value )
    {
        fill_missing_quality_ = value;
        return *this;
    }
 
    unsigned char fill_missing_quality() const
    {
        return fill_missing_quality_;
    }
 
    FastqWriter& repeat_label( bool value )
    {
        repeat_label_ = value;
        return *this;
    }
 
    bool repeat_label() const
    {
        return repeat_label_;
    }
 
    // ---------------------------------------------------------------------
    //     Internal Members
    // ---------------------------------------------------------------------
 
private:
 
    std::string make_filled_quality_string_(
        size_t length
    ) const;
 
    void write_sequence_(
        std::string const& label,
        std::string const& sites,
        std::string const& quality,
        std::ostream& os
    ) 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