File: CCSSequence.hpp

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#ifndef _BLASR_CCS_SEQUENCE_HPP_
#define _BLASR_CCS_SEQUENCE_HPP_

#include <pbdata/Enumerations.h>
#include <pbdata/SMRTSequence.hpp>
#include <pbdata/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_