config.hpp

#ifndef CONFIG_HPP
#define CONFIG_HPP

#include <string>
#include <vector>
#include <iostream>

#include "cxxopts.hpp"
#include "bed_utils.hpp"

using namespace std ;

class Configuration {

private:
    static Configuration* instance ;

public:
    static Configuration* getInstance() ;

    void parse(int argc, char* argv[]) ;

    int cutoff = 0 ;
    int overlap = -1 ;
    int threads = 4 ;
    int coverage = 50 ;
    int batch_size = 1000 ;
    int min_sv_length = 25 ;
    int min_indel_length = 20 ;
    int aggregate_batches = 5 ;
    int min_cluster_weight = 2 ;

    bool binary = false ;
    bool clipped = false ;
    bool putative = true ;
    bool assemble = false ;
    bool aggregate = false ;
    bool selective = true ;

    std::string bed ;
    std::string bam ; // reads bam (reconstructed or not)
    std::string sfsbam ; // superstrings bam (from realignment)
    std::string vcf ;
    std::string type ;
    std::string workdir ;
    std::string append ;
    std::string index ;
    std::string fastq ;
    std::string fasta ;
    std::string target ;
    std::string prefix ;
    std::string reference ;

private:

    Configuration() ;

    Configuration(Configuration const&) = delete ;
    void operator=(Configuration const&) = delete ;

    Configuration& operator[](std::string) ;
    
    cxxopts::Options parser ;
};

#endif