CCSSequence.hpp

#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:
	UInt numPasses;
	UInt 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;
	void Free(); 

	int GetStorageSize(); 
	//
	//
	// 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); 
};

#endif // _BLASR_CCS_SEQUENCE_HPP_