Recombination.hpp

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/*

Copyright (C) 2003-2009 Kevin Thornton, krthornt[]@[]uci.edu

Remove the brackets to email me.

This file is part of libsequence.

libsequence 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.

libsequence 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
long with libsequence.  If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef RECOMBINATION_H
#define RECOMBINATION_H

#include <vector>
#include <limits>

namespace Sequence
{
    struct PairwiseLDstats
    {
        double i;
                double j;
                double rsq;
                double D;
                double Dprime;
        bool skipped;
        PairwiseLDstats();
    };

    class PolyTable;
    namespace Recombination
    {
        double HudsonsC(const Sequence::PolyTable *data,
                        const bool &haveOutgroup, const unsigned &outgroup)__attribute__ ((deprecated));
        std::vector<PairwiseLDstats> Disequilibrium(
            const Sequence::PolyTable *data, const bool &haveOutgroup = false,
            const unsigned &outgroup = 0, const unsigned &mincount = 1,
            const double max_distance = std::numeric_limits<double>::max())__attribute__ ((deprecated));

        PairwiseLDstats PairwiseLD(const Sequence::PolyTable *data, unsigned i,
                                   unsigned j,
                                   const bool &haveOutgroup = false,
                                   const unsigned &outgroup = 0,
                                   const unsigned &mincount = 1,
                                   const double max_distance
                                   = std::numeric_limits<double>::max())__attribute__ ((deprecated));
    }
}
#endif