/usr/include/pbseq/pbdata/CCSSequence.hpp is in libpbdata-dev 0~20161219-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | #ifndef _BLASR_CCS_SEQUENCE_HPP_
#define _BLASR_CCS_SEQUENCE_HPP_
#include "Enumerations.h"
#include "SMRTSequence.hpp"
#include "VectorUtils.hpp"
//
// A CCS Sequence is both a SMRTSequence itself, and contains a list of SMRTSequences.
//
class CCSSequence : public SMRTSequence {
public:
int numPasses;
DNALength numConsensusBases;
std::vector<DNALength> passStartPulse, passNumPulses, passStartBase, passNumBases;
std::vector<Byte> passDirection;
std::vector<Byte> adapterHitBefore, adapterHitAfter, adapterHitConfidence;
//
// The CCS Sequence originates from a full length read. That read
// is stored here for reference later on. The ccs read is stored in
// the inherited fields from SMRTSequence so that it may be worked
// with as if it were a normal non-ccs sequence.
//
SMRTSequence unrolledRead;
public:
inline ~CCSSequence();
void Free();
UInt HoleNumber(void) const;
CCSSequence & HoleNumber(const UInt holeNumber);
int GetStorageSize();
/// \name
/// \{
/// 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 Explode(std::vector<SMRTSequence> &subreads);
/// \}
};
inline CCSSequence::~CCSSequence() {
CCSSequence::Free();
}
#endif // _BLASR_CCS_SEQUENCE_HPP_
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