// -*- 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 "blt_util/log.hh"
#include "blt_util/math_util.hh"
#include "blt_util/qscore.hh"
#include "blt_util/qscore_cache.hh"

#include <cstdlib>
#include <iostream>



qphred_cache::
qphred_cache() {
    for(int i(0);i<=MAX_QSCORE;++i){
        q2p[i] = phred_to_error_prob(static_cast<double>(i));
    }
    for(int i(0);i<=MAX_QSCORE;++i){
        q2lncompe[i] = log1p_switch(-q2p[i]);
    }
    static const double q2lnp(-std::log(10.)/10.);
    for(int i(0);i<=MAX_QSCORE;++i){
        q2lne[i] = static_cast<double>(i)*q2lnp;
    }

    for(int i(0);i<=MAX_QSCORE;++i){
        for(int j(0);j<=MAX_MAP;++j){
            mappedq[j][i] = error_prob_to_qphred(phred_to_mapped_error_prob(i,j));
        }
    }
}



void
qphred_cache::
qscore_error(const int qscore) const {
    log_os << "ERROR:: invalid phred qscore: " << qscore << "\n";
    exit(EXIT_FAILURE);
}



qlogodds_cache::
qlogodds_cache() : q2p(q2p_base-MIN_QSCORE) {
    for(int i(MIN_QSCORE);i<=MAX_QSCORE;++i){
        q2p[i] = logodds_to_error_prob(static_cast<double>(i));
    }
}



void
qlogodds_cache::
qscore_error(const int qscore) const {
    log_os << "ERROR:: invalid logodds qscore: " << qscore << "\n";
    exit(EXIT_FAILURE);
}