read_bases.h

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#ifndef gamgee__read_bases__guard
#define gamgee__read_bases__guard

#include "htslib/sam.h"

#include <memory>
#include <map>

namespace gamgee {

enum class Base { A = 1, C = 2, G = 4, T = 8, N = 15 };

class ReadBases {
public:
  explicit ReadBases(const std::shared_ptr<bam1_t>& sam_record);
  ReadBases(const ReadBases& other);
  ReadBases(ReadBases&& other) = default;
  ReadBases& operator=(const ReadBases& other);
  ReadBases& operator=(ReadBases&& other) = default;
  ~ReadBases() = default; 

  Base operator[](const uint32_t index) const;   
  void set_base(const uint32_t index, const Base base);  
  uint32_t size() const { return m_num_bases; }; 
  bool operator==(const ReadBases& other) const; 
  bool operator!=(const ReadBases& other) const; 
  std::string to_string() const;  

private:
  std::shared_ptr<bam1_t> m_sam_record; 
  uint8_t* m_bases;                     
  uint32_t m_num_bases;                 

  static const std::map<Base, const char*> base_to_string_map; 

  friend class SamBuilder; 
};

}

#endif /* gamgee__read_bases__guard */