sync_common.cpp

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/*
    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/formats/sync_common.hpp"
 
#include <iostream>
#include <stdexcept>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     PoPoolation2 Synchronized File Helper Functions
// =================================================================================================
 
std::ostream& to_sync( BaseCounts const& bs, std::ostream& os )
{
    os << bs.a_count << ":" << bs.t_count << ":" << bs.c_count << ":" << bs.g_count;
    os << ":" << bs.n_count << ":" << bs.d_count;
    return os;
}
 
std::ostream& to_sync( Variant const& var, std::ostream& os )
{
    os << var.chromosome << "\t" << var.position << "\t" << var.reference_base;
    for( auto const& bs : var.samples ) {
        os << "\t";
        to_sync( bs, os );
    }
    os << "\n";
    return os;
}
 
} // namespace population
} // namespace genesis