sv_data.h

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#ifndef SV_DATA_H
#define SV_DATA_H
 
#include "fasta_query.h"  // For querying the reference genome
#include "types.h"
 
#include <string>
#include <map>
 
 
class SVData {
    private:
        // SV candidate to read depth map
        SVDepthMap sv_calls;
                
        // Store a reference to the reference genome
        FASTAQuery *ref_genome;
 
        // SV type to string map
        std::map<int, std::string> sv_type_map = {
            {0, "DEL"},
            {1, "DUP"},
            {2, "INV"},
            {3, "INS"},
            {4, "BND"}
        };
        std::map<int, std::string> sv_type_map = {…};
        
    public:
        SVData(FASTAQuery& ref_genome);
        void addSVCall(std::string chr, int start, int end, int sv_type, std::string alt_allele);
        //void addSVCalls(SVData sv_calls);
 
        std::string getRefGenome();
        
        // Query the reference genome for a given sequence
        std::string getSequence(std::string chr, int pos_start, int pos_end);
 
        // Update the SV type for a given SV candidate
        void updateSVType(SVCandidate key, int sv_type);
        
        // Save SV calls to VCF
        void saveToVCF(FASTAQuery& ref_genome, std::string output_dir);
 
        // Begin and end iterators for the SV candidate map
        SVDepthMap::iterator begin() { return this->sv_calls.begin(); }
        SVDepthMap::iterator end() { return this->sv_calls.end(); }
};
class SVData {…};
 
#endif // SV_DATA_H