input_data.h

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//
// common.h:
// Manage common types, parameters, and functions
 
#ifndef INPUT_DATA_H
#define INPUT_DATA_H
 
#include "fasta_query.h"
 
#include <string>
#include <vector>
#include <map>
 
class InputData {
    public:
        InputData();
        std::string getBAMFilepath();
        void setBAMFilepath(std::string filepath);
        void setRefGenome(std::string fasta_filepath);
        FASTAQuery getRefGenome();
        std::string getSequence(std::string chr, int pos_start, int pos_end);
        std::string getOutputDir();
        void setOutputDir(std::string dirpath);
        std::string getRegion();
        void setRegion(std::string region);
        int getWindowSize();
        void setWindowSize(int window_size);
        std::string getSNPFilepath();
        void setSNPFilepath(std::string filepath);
        std::string getRegionChr();
        int getRegionStart();
        int getRegionEnd();
        bool getRegionSet();
        void setChrCov(std::string chr_cov);
        int getChrCov(std::string chr, double& cov);
        std::string getPFBFilepath();
        void setPFBFilepath(std::string filepath);
 
    private:
        std::string bam_filepath = "";
        std::string ref_filepath = "";
        std::string snp_vcf_filepath = "";
        std::string pfb_filepath = "";
        FASTAQuery fasta_query;
        std::string output_dir   = "";
        std::string region = "";
        int window_size = 10000;
        std::string region_chr = "";
        int region_start = 0;
        int region_end   = 0;
        bool region_set = false;
        std::map<std::string, double> chr_cov;
};
class InputData {…};
 
#endif // INPUT_DATA_H