clipper.hpp

#ifndef CLIPPER_HPP
#define CLIPPER_HPP

#include <map>
#include <set>
#include <omp.h>
#include <vector>
#include <string>
#include <unordered_map>

#include "htslib/sam.h"
#include "htslib/hts.h"
#include "interval_tree.hpp"

#include "sv.hpp"
#include "lprint.hpp"
#include "chromosomes.hpp"

struct Clip {
    std::string name ;
    std::string chrom ;
    uint p ;
    uint l ;
    bool starting ;
    uint w ;

    Clip() { 
        w = 0;
    }

    Clip(std::string name_, std::string chrom_, const uint p_, uint l_, bool starting_, uint w_ = 0) {
        name = name_ ;
        chrom = chrom_ ;
        p = p_ ;
        l = l_ ;
        starting = starting_ ;
        w = w_ ;
    }

    bool operator<(const Clip &c) const {
        return p < c.p;
    }
};

class Clipper {

private:
    std::vector<Clip> clips ;
    std::vector<Clip> remove_duplicates(const std::vector<Clip> &);
    std::vector<Clip> combine(const std::vector<Clip> &);
    std::vector<Clip> filter_lowcovered(const std::vector<Clip> &, const uint);
    std::vector<Clip> cluster(const std::vector<Clip> &, uint);
    std::vector<Clip> filter_tooclose_clips(const std::vector<Clip> &, lib_interval_tree::interval_tree_t<int> &);

public:
    std::vector<std::vector<SV>> _p_svs ;

    Clipper(const std::vector<Clip>&) ;
    void call(int threads, lib_interval_tree::interval_tree_t<int>&) ;
};

#endif