#include <pbdata/defs.h>
#include <pbdata/PrettyException.hpp>
#include <pbdata/qvs/QualityValue.hpp>

#include <cassert>
#include <cmath>

QualityValue ProbabilityToQualityValue(QualityProbability pErr, QVScale qvScale)
{
    if (qvScale == POverOneMinusP) {
        QualityProbability pe;
        QualityProbability maxReportedErrorProb = 0.499;
        pe = MIN(pErr, maxReportedErrorProb);
        return MIN(255, -100 * log10(pe / (1 - pe)));
    } else if (qvScale == PHRED) {
        return -10 * log10(pErr);
    } else {
        BLASR_THROW("Unknown qvScale!");
    }
}

QualityValue PacBioQVToPhred(QualityValue pbQV)
{
    // yanked from Aaron's code.
    return (unsigned char)floor(10.0 * log10(1.0 + pow(10.0, pbQV / 100.0)) + 0.5);
}

QualityValue ToPhred(QualityValue qv, QVScale qvScale)
{
    //
    // Nothing to do when the quality is already in phred.
    //
    if (qvScale == PHRED) {
        return qv;
    } else {
        return PacBioQVToPhred(qv);
    }
}

QualityProbability QualityValueToProbability(QualityValue qv, QVScale qvScale)
{
    if (qvScale == POverOneMinusP) {
        QualityProbability pp;
        pp = pow(10, qv / -100.0);
        return pp / (1 + pp);
    } else if (qvScale == PHRED) {
        return pow(10, qv / -10.0);
    } else {
        BLASR_THROW("Unknown qvScale!");
    }
}

QVScale DetermineQVScaleFromChangeListID(ChangeListID &cl)
{
    ChangeListID phredCL;
    phredCL.intVer.resize(3);
    phredCL.intVer[0] = 1;
    phredCL.intVer[1] = 2;
    phredCL.intVer[2] = 2;
    if (cl.LessThan(phredCL)) {
        return POverOneMinusP;
    } else {
        return PHRED;
    }
}