dict.hpp

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#ifndef GENESIS_SEQUENCE_FUNCTIONS_DICT_H_
#define GENESIS_SEQUENCE_FUNCTIONS_DICT_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/sequence/reference_genome.hpp"
#include "genesis/sequence/sequence_dict.hpp"
#include "genesis/sequence/sequence_set.hpp"
#include "genesis/utils/io/input_source.hpp"
 
#include <string>
#include <vector>
 
namespace genesis {
namespace sequence {
 
// =================================================================================================
//     Sequence Dict
// =================================================================================================
 
SequenceDict read_sequence_dict( std::shared_ptr<utils::BaseInputSource> source );
 
SequenceDict read_sequence_fai( std::shared_ptr<utils::BaseInputSource> source );
 
SequenceDict sequence_set_to_dict( SequenceSet const& set );
 
SequenceDict reference_genome_to_dict( ReferenceGenome const& rg );
 
// =================================================================================================
//     Reference
// =================================================================================================
 
enum class ReferenceComparisonMode
{
    kStrict,
 
    kLeftSuperset,
 
    kRightSuperset,
 
    kSharedOnly
};
 
bool compatible_references(
    SequenceDict const& lhs,
    SequenceDict const& rhs,
    ReferenceComparisonMode mode = ReferenceComparisonMode::kStrict
);
 
bool verify( SequenceDict const& dict, SequenceSet const& set, bool match_first_word = false );
 
} // namespace sequence
} // namespace genesis
 
#endif // include guard