simple_pileup_common.hpp

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#ifndef GENESIS_POPULATION_FORMAT_SIMPLE_PILEUP_COMMON_H_
#define GENESIS_POPULATION_FORMAT_SIMPLE_PILEUP_COMMON_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/population/format/simple_pileup_reader.hpp"
#include "genesis/sequence/functions/quality.hpp"
 
#include <string>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Simple (m)pileup Reader Helper Functions
// =================================================================================================
 
SampleCounts convert_to_sample_counts(
    SimplePileupReader::Sample const& sample,
    unsigned char min_phred_score = 0
);
 
Variant convert_to_variant(
    SimplePileupReader::Record const& record,
    unsigned char min_phred_score = 0
);
 
genesis::sequence::QualityEncoding guess_pileup_quality_encoding(
    std::shared_ptr< utils::BaseInputSource > source,
    size_t max_lines = 0
);
 
} // namespace population
} // namespace genesis
 
#endif // include guard