// -*- 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 __POSITION_SNP_CALL_PPROB_DIGT_HH
#define __POSITION_SNP_CALL_PPROB_DIGT_HH

#include "blt_common/blt_shared.hh"
#include "blt_common/snp_pos_info.hh"

#include "blt_util/digt.hh"
#include "blt_util/qscore.hh"

#include <boost/utility.hpp>

#include <iosfwd>



struct diploid_genotype : private boost::noncopyable {

    diploid_genotype() : is_snp(false), ref_gt(0), max_gt(0), max2_gt(0), max_gt_poly(0) {
        static const double p(1./static_cast<double>(DIGT::SIZE));
        static const int qp(error_prob_to_qphred((1.-p)));
        snp_qphred=qp;
        max_gt_qphred=qp;
        max_gt_poly_qphred=qp;
        for(unsigned i(0);i<DIGT::SIZE;++i) {
            pprob[i] = p;
            pprob_poly[i] = p;
        }
    }

    bool is_snp;
    unsigned ref_gt;
    unsigned max_gt;
    unsigned max2_gt;
    unsigned max_gt_poly;
    int snp_qphred;
    int max_gt_qphred;
    int max_gt_poly_qphred;
    double pprob[DIGT::SIZE];
    double pprob_poly[DIGT::SIZE];
};

// debuging output -- produces labels
//
std::ostream& operator<<(std::ostream& os,const diploid_genotype& dgt);


// allele call output:
//
void
write_diploid_genotype_allele(const blt_options& opt,
                              const snp_pos_info& pi,
                              const diploid_genotype& dgt,
                              std::ostream& os);

// snp call output:
//
inline
void
write_diploid_genotype_snp(const blt_options& opt,
                           const snp_pos_info& pi,
                           const diploid_genotype& dgt,
                           std::ostream& os){

    write_diploid_genotype_allele(opt,pi,dgt,os);
}

/// \brief call a snp @ pos by calculating the posterior probability
/// of all possible genotypes for a diploid individual.
///
/// When is_always_test is true, probabilities are calculated even
/// when a snp could not exist at the site.
///
void
position_snp_call_pprob_digt(const double theta,
                             const snp_pos_info& pi,
                             const std::vector<float>& dependent_eprob,
                             diploid_genotype& dgt,
                             const bool is_always_test = false);

#endif