marker_traits.hpp

// Copyright 2021 Arnaud Becheler    <abechele@umich.edu> Florence Jornod <florence@jornod.com>
 
/*********************************************************************** * 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 2 of the License, or    * (at your option) any later version. *
 *                                                                      *
 ************************************************************************/
 
#ifndef __GENET_H_INCLUDED__
#define __GENET_H_INCLUDED__
 
/**************************************************************************
    Descriptor for marker types used in genetic sample data :
     - In microsatellite data, allelic states are unsigned integers
     - In Single Nuclear Polymorphism data, allelic states are A, T, G, C
***************************************************************************/
 
namespace quetzal::format
{
namespace genetics
{
 
template <typename T> struct Marker_Descriptor
{
    typedef T value_type;
};
 
Marker_Descriptor<unsigned int> microsat_instance;
Marker_Descriptor<std::string> SNP_instance;
 
using undefined = int;
using microsatellite = Marker_Descriptor<unsigned int>;
using SNP = Marker_Descriptor<std::string>;
 
} // namespace genetics
} // namespace quetzal::format
 
#endif