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#include <math.h>
#include "../defs.h"
#include <assert.h>
#include "QualityValue.hpp"
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 {
assert(false);
}
}
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 {
assert(false);
}
}
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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