sam_writer.h

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#ifndef gamgee__sam_writer__guard
#define gamgee__sam_writer__guard

#include <string>
#include <memory>

#include "sam.h"
#include "sam_header.h"

#include "../utils/hts_memory.h"

#include "htslib/sam.h"

namespace gamgee {

class SamWriter {

 public: 

  explicit SamWriter(const std::string& output_fname = "-", const bool binary = true);

  explicit SamWriter(const SamHeader& header, const std::string& output_fname = "-", const bool binary = true);

  SamWriter(const SamWriter& other) = delete;
  SamWriter& operator=(const SamWriter& other) = delete;

  SamWriter(SamWriter&& other) = default;
  SamWriter& operator=(SamWriter&& other) = default;

  void add_record(const Sam& body);

  void add_header(const SamHeader& header);

 private:
  std::unique_ptr<htsFile, utils::HtsFileDeleter> m_out_file;  
  SamHeader m_header;                   

  static htsFile* open_file(const std::string& output_fname, const std::string& binary);
  void write_header() const;

};

}

#endif // gamgee__sam_writer__guard