// -*- 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
///

#include "starling/starling_shared.hh"

#include <cmath>

#include <iostream>



void
get_starling_deriv_options(const starling_options& client_opt,
                           const pos_t ref_size,
                           starling_deriv_options& client_dopt){

    get_blt_deriv_options(client_opt,ref_size,client_dopt);

    {
        // get read path posterior probs:
        const double site_prior(1./(2.*static_cast<double>(client_opt.genome_size)));
        client_dopt.site_lnprior=std::log(site_prior);
        client_dopt.nonsite_lnprior=std::log(1.-site_prior);
    }

    {
        // get diploid indel prior:
        //
        double* prior(client_dopt.diploid_indel_state_lnprior);
        const double theta(client_opt.bindel_diploid_theta);

        prior[DIINDEL::NOINDEL]=1.-(3.*theta)/2.;
        prior[DIINDEL::HOM]=theta/2.;
        prior[DIINDEL::HET]=theta;
     
        for(unsigned gt(0);gt<DIINDEL::SIZE;++gt){
            prior[gt] = std::log(prior[gt]);
        }
    }
}



void
starling_read_counts::
report(std::ostream& os) const {
    blt_read_counts::report(os);
    os << "STARLING_READ_COUNTS"
       << " normal_indel_used: " << normal_indel_used
       << " normal_indel_intersect: " << normal_indel_intersect
       << " grouper_indel_used: " << grouper_indel_used
       << " grouper_indel_intersect: " << grouper_indel_intersect
       << " grouper_unused: " << grouper_unused << "\n";
}