sample_counts.hpp

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#ifndef GENESIS_POPULATION_SAMPLE_COUNTS_H_
#define GENESIS_POPULATION_SAMPLE_COUNTS_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/filter/filter_status.hpp"
 
#include <array>
#include <string>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Sample Counts
// =================================================================================================
 
struct SampleCounts
{
    using size_type = size_t;
 
    size_type a_count = 0;
 
    size_type c_count = 0;
 
    size_type g_count = 0;
 
    size_type t_count = 0;
 
    size_type n_count = 0;
 
    size_type d_count = 0;
 
    FilterStatus status;
 
};
 
// =================================================================================================
//     Sorted Sample Counts
// =================================================================================================
 
struct SortedSampleCounts
{
    struct BaseCount
    {
        char   base;
        size_t count;
 
        BaseCount()
            : base('N')
            , count(0)
        {}
 
        BaseCount( char b, size_t c )
            : base(b)
            , count(c)
        {}
    };
 
    SortedSampleCounts() = default;
 
    SortedSampleCounts(
        char b0, size_t c0, char b1, size_t c1, char b2, size_t c2, char b3, size_t c3
    )
        : data( std::array<BaseCount, 4>{{
            BaseCount{ b0, c0 }, BaseCount{ b1, c1 }, BaseCount{ b2, c2 }, BaseCount{ b3, c3 },
        }})
    {}
 
    BaseCount& operator[]( size_t index )
    {
        return data[index];
    }
 
    BaseCount const& operator[]( size_t index ) const
    {
        return data[index];
    }
 
    std::array<BaseCount, 4> data;
};
 
} // namespace population
} // namespace genesis
 
#endif // include guard