sv_caller.h

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// SVCaller: Detect SVs from long read alignments
 
#ifndef SV_CALLER_H
#define SV_CALLER_H
 
#include "input_data.h"
#include "cnv_data.h"
#include "sv_data.h"
#include "types.h"
 
 
class SVCaller {
    private:
        //int max_indel_dist = 1000;  // Maximum distance between two indels to
        //be considered as a single SV
        int max_indel_dist = 10;  // Maximum distance between two indels to be considered as a single SV
        //int min_sv_size = 50;       // Minimum SV size to be considered
        //int min_sv_size = 30;       // Minimum SV size to be considered
        int min_sv_size = 50;       // Minimum SV size to be considered
        int min_mapq = 20;          // Minimum mapping quality to be considered
        InputData* input_data;
 
        // Detect SVs from long read alignments in the CIGAR string
        SVData detectSVsFromCIGAR(std::string chr, int32_t pos, uint32_t* cigar, int cigar_len);
 
        // Detect SVs from split-read alignments (primary and supplementary)
        SVData detectSVsFromSplitReads();
 
    public:
        SVCaller(InputData& input_data);
 
        // Detect SVs and predict SV type from long read alignments and CNV calls
        SVData run();
};
class SVCaller {…};
 
#endif // SV_CALLER_H