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#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;
}
}
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