quality.hpp

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#ifndef GENESIS_SEQUENCE_FUNCTIONS_QUALITY_H_
#define GENESIS_SEQUENCE_FUNCTIONS_QUALITY_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 <array>
#include <iosfwd>
#include <memory>
#include <stdexcept>
#include <string>
#include <vector>

namespace genesis {

// =================================================================================================
//     Forward declarations
// =================================================================================================

namespace utils {
    class BaseInputSource;
}

namespace sequence {

// =================================================================================================
//     Quality Encoding and Decoding
// =================================================================================================

enum class QualityEncoding
{
    kSanger,
    kSolexa,
    kIllumina13,
    kIllumina15,
    kIllumina18
};

std::string quality_encoding_name( QualityEncoding encoding );

unsigned char quality_decode_to_phred_score(
    char quality_code,
    QualityEncoding encoding = QualityEncoding::kSanger
);

std::vector<unsigned char> quality_decode_to_phred_score(
    std::string const& quality_codes,
    QualityEncoding encoding = QualityEncoding::kSanger
);

inline char quality_encode_from_phred_score( unsigned char phred_score, bool clamp = true )
{
    // Only do one branch here, as this should be rare case, and then test and branch again inside.
    if( phred_score > 93 ) {
        if( clamp ) {
            phred_score = std::min( phred_score, static_cast<unsigned char>(93) );
        } else {
            throw std::invalid_argument(
                "Cannot encode phred score outside of [0, 93] to Sanger format."
            );
        }
    }
    return static_cast<char>( phred_score + 33 );
}

inline std::string quality_encode_from_phred_score(
    std::vector<unsigned char> const& phred_scores,
    bool clamp = true
) {
    auto qualities = std::string( phred_scores.size(), ' ' );
    for( size_t i = 0; i < phred_scores.size(); ++i ) {
        qualities[i] = quality_encode_from_phred_score( phred_scores[i], clamp );
    }
    return qualities;
}

// =================================================================================================
//     Guess Quality Encoding Type
// =================================================================================================

QualityEncoding guess_fastq_quality_encoding( std::array<size_t, 128> const& char_counts );

QualityEncoding guess_fastq_quality_encoding( std::shared_ptr< utils::BaseInputSource > source );

// =================================================================================================
//     Quality Computations
// =================================================================================================

unsigned char error_probability_to_phred_score( double error_probability );

double phred_score_to_error_probability( unsigned char phred_score );

signed char error_probability_to_solexa_score( double error_probability );

double solexa_score_to_error_probability( signed char solexa_score );

signed char phred_score_to_solexa_score( unsigned char phred_score );

unsigned char solexa_score_to_phred_score( signed char solexa_score );

} // namespace sequence
} // namespace genesis

#endif // include guard