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#include <alignment/qvs/QualityValueProfile.hpp>
QualityValueProfile::QualityValueProfile(int _wordSize, int _numQualityValues)
{
wordSize = _wordSize;
numQualityValues = _numQualityValues;
// Initialize the tuple metrics to map from seq->index
tm.Initialize(wordSize);
nWords = 1 << (2 * wordSize);
// Initialize the matrix of quality values.
profile.Grow(nWords, numQualityValues);
profile.Initialize(0);
}
void QualityValueProfile::Update(Nucleotide *seq, QualityValue qv)
{
DNATuple tuple;
if (tuple.FromStringLR(seq, tm)) {
profile.Set(tuple.tuple, qv, profile(tuple.tuple, qv) + 1);
}
}
void QualityValueProfile::Print(std::ofstream &out)
{
out << wordSize << " " << numQualityValues << " " << CDF_GRANULARITY << std::endl;
profile.Print(out);
}
void QualityValueProfile::ProfileToCDF()
{
int qv;
int wordIndex;
for (wordIndex = 0; wordIndex < nWords; wordIndex++) {
int totalSamples = 0;
for (qv = 0; qv < numQualityValues; qv++) {
totalSamples += profile(wordIndex, qv);
profile.Set(wordIndex, qv, totalSamples);
}
for (qv = 0; qv < numQualityValues; qv++) {
profile.Set(wordIndex, qv,
((profile(wordIndex, qv) * 1.0) / totalSamples) * CDF_GRANULARITY);
}
}
}
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