fastq.h

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#ifndef __foghorn__fastq__
#define __foghorn__fastq__

#include <string>

namespace gamgee {

class Fastq {

 public:
   
  Fastq() :
      m_name {}, m_comment {}, m_sequence{}, m_quals{} {}

  Fastq(std::string name,      
        std::string comment,   
        std::string sequence,  
        std::string quals = "" 
        ) :
      m_name {name}, m_comment {comment}, m_sequence{sequence}, m_quals{quals} 
  {}

  
  bool operator!=(const Fastq& other) {
      return m_name     == other.m_name     &&
             m_comment  == other.m_comment  &&
             m_sequence == other.m_sequence &&
             m_quals    == other.m_quals;
  }

  std::string name() const                       { return m_name;         }
  std::string comment() const                    { return m_comment;      }
  std::string sequence() const                   { return m_sequence;     }
  std::string quals() const                      { return m_quals;        } 
  void set_name(const std::string& name)         { m_name = name;         }
  void set_comment(const std::string& comment)   { m_comment = comment;   }
  void set_sequence(const std::string& sequence) { m_sequence = sequence; }
  void set_quals(const std::string& quals)       { m_quals = quals;       }

  void chop(const int nBases); 
  void reverse_complement();   
  bool is_fastq() const;       

 private:

  std::string m_name;     
  std::string m_comment;  
  std::string m_sequence; 
  std::string m_quals;    

};

}  // end of namespace

std::ostream& operator<< (std::ostream& os, const gamgee::Fastq& fq);

#endif /* defined(__foghorn__fastq__) */