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#include <pbdata/CCSSequence.hpp>
void CCSSequence::Free()
{
numPasses = 0;
numConsensusBases = 0;
SMRTSequence::Free();
unrolledRead.Free();
}
int CCSSequence::GetStorageSize()
{
return SMRTSequence::GetStorageSize() + unrolledRead.GetStorageSize();
}
UInt CCSSequence::HoleNumber(void) const { return SMRTSequence::HoleNumber(); }
CCSSequence &CCSSequence::HoleNumber(const UInt holeNumber)
{
SMRTSequence::HoleNumber(holeNumber);
unrolledRead.HoleNumber(holeNumber);
return *this;
}
//
// In the first iteration, Explode simply pulls the subreads out
// that are used in the ccs. Eventually, it will pull out all
// high-quality subreads.
//
void CCSSequence::Explode(std::vector<SMRTSequence> &subreads)
{
subreads.resize(numPasses);
int subreadIndex;
for (subreadIndex = 0; subreadIndex < numPasses; subreadIndex++) {
subreads[subreadIndex].ReferenceSubstring(this->unrolledRead, passStartBase[subreadIndex],
passNumBases[subreadIndex]);
subreads[subreadIndex].zmwData = unrolledRead.zmwData;
}
}
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