Class ChrCopyNumber

src/ChrCopyNumber.h:18–204

#include "ThreadPool.h"

class ChrCopyNumber
{
public:
	ChrCopyNumber(void);
	ChrCopyNumber(std::string const& chrName);
	ChrCopyNumber(int windowSize, int chrLength, std::string const& chrName);
	ChrCopyNumber(int windowSize, int chrLength, std::string const& chrName, int step, std::string targetBed = "");
	~ChrCopyNumber(void);
	void mappedPlusOneAtI(int i, int step, int l = -1);

	void addBAFinfo(SNPinGenome & snpingenome,int indexSNP);

	void fillInRatio(bool islog);
	void calculateRatio(ChrCopyNumber control, float normalizationConst) ;
	void recalculateRatio (float constant);
	void recalculateLogRatio (float constant) ;
	void recalculateRatioWithContam(float contamination, float normGenytype, bool isLogged);
    void recalculateRatio(ChrCopyNumber control);
	void calculateRatio(ChrCopyNumber control, double a0, double a1);
	void calculateRatio(ChrCopyNumber control, const double * a, const int degree);
	void calculateRatioLog(ChrCopyNumber control, const double * a, const int degree);
	int calculateBreakpoints(double breakPointThreshold, int firstChrLength, int breakPointType);
    int calculateBAFBreakpoints(double breakPointThreshold, int firstChrLength, int breakPointType);
	double calculateXiSum(int ploidy, std::map <float,float> &sds, std::map <float,float> &meds);
	double calculateXiSum(int ploidy, std::map <float,float> &sds);
	void calculateCopyNumberMedian(); //create median profiles using 'bpfinal_' and store them in medianProfile_, info about medians themselves is stored in medianValues_ and about SD in sd_, lengths of fragments in bpLengths_
	void calculateCopyNumberMedian(int ploidy, int minCNAlength, bool noisyData, bool CompleteGenomicsData, bool isLogged); //create median profiles as calculateCopyNumberMedian(), but merges close regions (roundByPloidy(median))
    void recalcFlanksForIndeces (int i, int j);
    void recalcFlanks(int telo_centromeric_flanks, int minNumberOfWindows); //merge short notNA-segments around NA-segments

	//void calculateRatio(double a,double b, double c, double d); //depreciated
	void calculateRatio(double *a, int degree);
    void recalculateRatio(double *a, int degree);

    void removeLowReadCountWindows(ChrCopyNumber control, const int RCThresh);
    void removeLowReadCountWindows(const int RCThresh) ;

	void deleteFlanks(int telo_centromeric_flanks);
	void deleteFragment(int i) ;
    int removeLargeExons(float threshold);

    std::string getGeneNameAtBin(int i);
	float		getValueAt(int i);
	int			getCoordinateAtBin(int i);
	int			getEndAtBin(int i);
	//void printLog2Ratio(std::ofstream const& file) ;
	float		getRatioAtBin(int i);
	std::vector <float>	getRatio();
	int			getLength();
    int         getChrLength();
	std::string getChromosome();
	int getCoveredPart(int breakPointStart, int breakPointEnd);//for exome-seq: get length of the genome covered by the targeted region (from breakPointStart to breakPointEnd)
	std::vector <float> getValues(); //get readCount_
	float		getMedianProfileAtI (int i) ;
	std::vector <float> getMedianValues () ;
	float getMedianValuesAt (int i) ;
	std::vector <float> getSDs ();//unUsed
	std::vector <int> getFragmentLengths_notNA ();