// -*- mode: c++; indent-tabs-mode: nil; -*-
//
// Copyright 2009 Illumina, Inc.
//
// This software is covered by the "Illumina Genome Analyzer Software
// License Agreement" and the "Illumina Source Code License Agreement",
// and certain third party copyright/licenses, and any user of this
// source file is bound by the terms therein (see accompanying files
// Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
// Illumina_Source_Code_License_Agreement.pdf and third party
// copyright/license notices).
//
//

/// \file

/// \author Chris Saunders
///
#ifndef __MONOGT_HH
#define __MONOGT_HH


namespace MONOGT {
    enum index_t {
        A,
        C,
        G,
        T,
        SIZE
    };

    inline
    const char*
    label(const unsigned idx){
        switch(idx){
        case A: return "A";
        case C: return "C";
        case G: return "G";
        case T: return "T";
        default: return "X";
        }
    }

    // the lhood function is no longer so general that these values can actually be changed...
    inline
    double
    expect(const int base_id,
           const int gt) {

        static const unsigned N_BASE(4);

        static const double ex[SIZE][N_BASE] = {{ 1.0, 0.0, 0.0, 0.0},
                                                { 0.0, 1.0, 0.0, 0.0},
                                                { 0.0, 0.0, 1.0, 0.0},
                                                { 0.0, 0.0, 0.0, 1.0}};

        return ex[gt][base_id];
    }
}


#endif