text: //
  // Created by Andreas Denger on 11.06.2017.
  //
  
  #ifndef ASSEMBLE_ASSEMBLER_H
  #define ASSEMBLE_ASSEMBLER_H
  
  #include "DBG.h"
  #include <vector>
  
  class DNA;
  
  class Assembler {
  public:
      /**
       * Find all linear stretches in dbg with average coverage >= cutoff
       * @param dbg A de Bruijn graph containing kmers
       * @param coverage_cutoff The lowest possible avg. coverage that any returned contig is allowed to have
       * @param sequences The assembled and valid contigs are written here
       */
      void assemble(const DBG &dbg, const unsigned coverage_cutoff, std::vector<std::string> &sequences) const;
  };
  
  
  #endif //ASSEMBLE_ASSEMBLER_H
  