cnv_caller.h

Go to the documentation of this file.

// CNVCaller: Detect CNVs and return the state sequence by SNP position
// (key = [chromosome, SNP position], value = state)
 
#ifndef CNV_CALLER_H
#define CNV_CALLER_H
 
#include "khmm.h"
#include "input_data.h"
#include "cnv_data.h"
 
#include <string>
#include <vector>
 
 
class CNVCaller {
    private:
        InputData* input_data;
        double chr_mean_coverage = 0;
 
    public:
        CNVCaller(InputData& input_data);
 
        // Detect CNVs and return the state sequence by SNP position
        // (key = [chromosome, SNP position], value = state)
        CNVData run();
 
        // Calculate Log R Ratios
        std::vector<double> calculateLogRRatiosAtSNPS(std::vector<int> snp_positions);
 
        // Calculate the mean chromosome coverage
        double calculateMeanChromosomeCoverage();
 
        // Calculate region mean coverage
        double calculateWindowLogRRatio(double mean_chr_cov, int start_pos, int end_pos);
 
        // Read SNP positions and BAF values from the VCF file
        std::pair<std::vector<int>, std::vector<double>> readSNPBAFs();
 
        // Read SNP population frequencies from the PFB file and return a vector
        // of population frequencies for each SNP location
        std::vector<double> getSNPPopulationFrequencies(std::vector<int> snp_locations);
 
        // Save a CSV with SNP positions, BAF values and Log R Ratios
        void saveToTSV(std::string filepath, std::vector<int> snp_locations, std::vector<double> bafs, std::vector<double> logr_ratios, std::vector<int> state_sequence);
};
class CNVCaller {…};
 
#endif // CNV_CALLER_H