Class ComplementFile

src/complementFile/complementFile.h:20–50

class RecordOutputMgr;

class ComplementFile : public ToolBase {

public:
  ComplementFile(ContextComplement *context);
  virtual ~ComplementFile();
	virtual bool init();
	virtual bool findNext(RecordKeyVector &hits);
	virtual void processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits);
  virtual void checkCoordinatesAgainstChromLength(const Record *rec);
	virtual void cleanupHits(RecordKeyVector &hits);
	virtual bool finalizeCalculations() {return true;}
	virtual void giveFinalReport(RecordOutputMgr *outputMgr);


protected:
	FileRecordMergeMgr *_frm;
	Bed3Interval _outRecord;
	string _currChrom;
	const NewGenomeFile *_genomeFile;
	CHRPOS _currStartPos;
  bool _onlyChromsWithBedRecords;
	RecordOutputMgr *_outputMgr;
	const vector<string> &_chromList;
	int _currPosInGenomeList;

	virtual ContextComplement *upCast(ContextBase *context) { return static_cast<ContextComplement *>(context); }

	void outPutLastRecordInPrevChrom();
	bool fastForward(const string &newChrom);
	void printRecord(CHRPOS endPos);
};