fastq_reader.hpp

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#ifndef GENESIS_SEQUENCE_FORMATS_FASTQ_READER_H_
#define GENESIS_SEQUENCE_FORMATS_FASTQ_READER_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 <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/sequence/functions/quality.hpp"
#include "genesis/sequence/sequence.hpp"
#include "genesis/utils/tools/char_lookup.hpp"
#include "genesis/utils/io/input_source.hpp"
 
#include <functional>
#include <iosfwd>
#include <memory>
#include <string>
 
namespace genesis {
 
// =================================================================================================
//     Forward Declarations
// =================================================================================================
 
namespace utils {
    class InputStream;
}
 
namespace sequence {
    class SequenceSet;
    class Sequence;
}
 
// =================================================================================================
//     Fastq Reader
// =================================================================================================
 
namespace sequence {
 
class FastqReader
{
public:
 
    // ---------------------------------------------------------------------
    //     Typedefs and Enums
    // ---------------------------------------------------------------------
 
    using quality_string_function = std::function< void(
        std::string const& quality_string, Sequence& sequence
    ) >;
 
    enum class SiteCasing
    {
        kUnchanged,
 
        kToUpper,
 
        kToLower
    };
 
    // ---------------------------------------------------------------------
    //     Constructor and Rule of Five
    // ---------------------------------------------------------------------
 
    FastqReader();
    ~FastqReader() = default;
 
    FastqReader( FastqReader const& ) = default;
    FastqReader( FastqReader&& )      = default;
 
    FastqReader& operator= ( FastqReader const& ) = default;
    FastqReader& operator= ( FastqReader&& )      = default;
 
    // ---------------------------------------------------------------------
    //     Reading
    // ---------------------------------------------------------------------
 
    SequenceSet read( std::shared_ptr< utils::BaseInputSource > source ) const;
 
    void read( std::shared_ptr< utils::BaseInputSource > source, SequenceSet& sequence_set ) const;
 
    // ---------------------------------------------------------------------
    //     Parsing
    // ---------------------------------------------------------------------
 
    void parse_document(
        utils::InputStream& input_stream,
        SequenceSet&        sequence_set
    ) const;
 
    bool parse_sequence(
        utils::InputStream& input_stream,
        Sequence&           sequence
    ) const;
 
protected:
 
    bool parse_sequence_( utils::InputStream& input_stream, Sequence& sequence ) const;
 
    void parse_label1_(   utils::InputStream& input_stream, Sequence& sequence ) const;
 
    void parse_sites_(    utils::InputStream& input_stream, Sequence& sequence ) const;
 
    void parse_label2_(   utils::InputStream& input_stream, Sequence& sequence ) const;
 
    void parse_quality_(  utils::InputStream& input_stream, Sequence& sequence ) const;
 
    // ---------------------------------------------------------------------
    //     Properties
    // ---------------------------------------------------------------------
 
public:
 
    FastqReader& site_casing( SiteCasing value );
 
    SiteCasing site_casing() const;
 
    FastqReader& valid_chars( std::string const& chars );
 
    std::string  valid_chars() const;
 
    utils::CharLookup<bool>& valid_char_lookup();
 
    FastqReader& quality_encoding( QualityEncoding encoding );
 
    QualityEncoding quality_encoding();
 
    FastqReader& quality_string_plugin( quality_string_function const& plugin );
 
    // ---------------------------------------------------------------------
    //     Members
    // ---------------------------------------------------------------------
 
private:
 
    SiteCasing              site_casing_      = SiteCasing::kUnchanged;
    bool                    use_validation_   = false;
    utils::CharLookup<bool> lookup_;
 
    QualityEncoding         quality_encoding_ = QualityEncoding::kSanger;
 
    // Functional that can be set to process the quality string found in fastq files.
    quality_string_function quality_string_plugin_ = [&](
        std::string const& quality_string, Sequence& sequence
    ){
        sequence.phred_scores( quality_decode_to_phred_score( quality_string, quality_encoding_ ));
    };
 
    // Internal reading buffer
    mutable std::string buffer_;
 
};
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard