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#include <alignment/simulator/QualitySample.hpp>
void QualitySample::CopyFromSequence(SMRTSequence &seq, int pos)
{
qv[0] = seq.qual[pos];
qv[1] = seq.deletionQV[pos];
qv[2] = seq.insertionQV[pos];
qv[3] = seq.substitutionQV[pos];
tags[0] = seq.deletionTag[pos];
tags[1] = seq.substitutionTag[pos];
frameValues[0] = seq.pulseIndex[pos];
frameValues[1] = seq.preBaseFrames[pos];
frameValues[2] = seq.widthInFrames[pos];
}
void QualitySample::Write(std::ofstream &out)
{
out.write((char *)qv, sizeof(qv[0]) * NQV);
out.write((char *)frameValues, sizeof(frameValues[0]) * NFV);
out.write((char *)tags, sizeof(tags[0]) * NT);
}
void QualitySample::Read(std::ifstream &in)
{
in.read((char *)qv, sizeof(QualityValue) * NQV);
in.read((char *)frameValues, sizeof(frameValues[0]) * NFV);
in.read((char *)tags, sizeof(tags[0]) * NT);
}
void QualitySample::CreateFromRead(SMRTSequence &seq, DNALength pos)
{
/*
* For now create with a static set of values:
* qvs:
* 0 QualityValue
* 1 DeletionQV
* 2 InsertionQV
* 3 SubstitutionQV
* tags:
* 0 DeletionTag
* 1 SubstitutionTag
* PulseData
* 0 PulseIndex
* 1 PreBaseFrames
* 2 WidthInFrames
*/
// qv.resize(4);
std::fill(&qv[0], &qv[NQV], 0);
if (seq.qual.Empty() == false) {
qv[0] = seq.qual[pos];
}
if (seq.deletionQV.Empty() == false) {
qv[1] = seq.deletionQV[pos];
}
if (seq.insertionQV.Empty() == false) {
qv[2] = seq.insertionQV[pos];
}
if (seq.substitutionQV.Empty() == false) {
qv[3] = seq.substitutionQV[pos];
}
std::fill(&tags[0], &tags[NT], 0);
if (seq.deletionTag) {
tags[0] = seq.deletionTag[pos];
}
if (seq.substitutionTag) {
tags[1] = seq.substitutionTag[pos];
}
std::fill(&frameValues[0], &frameValues[NFV], 0);
if (seq.pulseIndex) {
frameValues[0] = seq.pulseIndex[pos];
}
if (seq.preBaseFrames) {
frameValues[1] = seq.preBaseFrames[pos];
}
if (seq.widthInFrames) {
frameValues[2] = seq.widthInFrames[pos];
}
}
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