variant.hpp

Go to the documentation of this file.

#ifndef GENESIS_POPULATION_VARIANT_H_
#define GENESIS_POPULATION_VARIANT_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/sample_counts.hpp"
#include "genesis/population/filter/filter_status.hpp"
 
#include <string>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Variant
// =================================================================================================
 
struct Variant
{
    // Internal memory layout: The status is 4 bytes, which we put next to the two one-byte members,
    // so that we do not get extra alignment padding here, to keep the data structure small.
    // Unfortunately, in release buiild, we are still a bit bigger than a cache line of 64 byte,
    // but short of making position a 32 bit number, there is nothing we can do about that.
    // Not sure if that would improve performance in our case anyway. Could be tested.
 
    std::string chromosome;
    size_t      position = 0;
 
    FilterStatus status;
    static_assert( sizeof(FilterStatus) == 4, "sizeof(FilterStatus) != 4" );
 
    char        reference_base   = 'N';
    char        alternative_base = 'N';
 
    std::vector<SampleCounts> samples;
};
 
} // namespace population
} // namespace genesis
 
#endif // include guard