population/functions/functions.hpp

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#ifndef GENESIS_POPULATION_FUNCTIONS_FUNCTIONS_H_
#define GENESIS_POPULATION_FUNCTIONS_FUNCTIONS_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2022 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/base_counts.hpp"
#include "genesis/population/variant.hpp"
 
#include <array>
#include <iosfwd>
#include <utility>
#include <string>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Status and Information
// =================================================================================================
 
struct BaseCountsStatus
{
    bool is_covered = false;
 
    bool is_snp = false;
 
    bool is_biallelic = false;
 
    bool is_ignored = false;
};
 
BaseCountsStatus status(
    BaseCounts const& sample,
    size_t min_coverage = 0,
    size_t max_coverage = 0,
    size_t min_count = 0,
    bool tolerate_deletions = false
);
 
// =================================================================================================
//     Counts
// =================================================================================================
 
size_t get_base_count( BaseCounts const& bc, char base );
 
BaseCounts total_base_counts( Variant const& variant );
 
// =================================================================================================
//     Sorting
// =================================================================================================
 
SortedBaseCounts sorted_base_counts( BaseCounts const& sample );
 
std::pair<SortedBaseCounts, SortedBaseCounts> sorted_average_base_counts(
    BaseCounts const& sample_a,
    BaseCounts const& sample_b
);
 
SortedBaseCounts sorted_base_counts(
    Variant const& variant, bool reference_first
);
 
// =================================================================================================
//     Merging
// =================================================================================================
 
inline size_t nucleotide_sum( BaseCounts const& sample )
{
    return sample.a_count + sample.c_count + sample.g_count + sample.t_count;
}
 
inline size_t total_nucleotide_sum( Variant const& variant )
{
    return nucleotide_sum( total_base_counts( variant ));
}
 
void merge_inplace( BaseCounts& p1, BaseCounts const& p2 );
 
BaseCounts merge( BaseCounts const& p1, BaseCounts const& p2 );
 
BaseCounts merge( std::vector<BaseCounts> const& p );
 
// =================================================================================================
//     Consensus
// =================================================================================================
 
std::pair<char, double> consensus( BaseCounts const& sample );
 
std::pair<char, double> consensus( BaseCounts const& sample, BaseCountsStatus const& status );
 
char guess_reference_base( Variant const& variant );
 
char guess_alternative_base( Variant const& variant, bool force = true );
 
// =================================================================================================
//     Output
// =================================================================================================
 
std::ostream& operator<<( std::ostream& os, BaseCounts const& bs );
 
} // namespace population
} // namespace genesis
 
#endif // include guard