variant_writer.h

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#ifndef gamgee__variant_writer__guard
#define gamgee__variant_writer__guard

#include <string>
#include <memory>
#include <zlib.h>

#include "variant.h"
#include "variant_header.h"

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

#include "htslib/vcf.h"

namespace gamgee {

class VariantWriter {

 public: 

  explicit VariantWriter(const std::string& output_fname = "-", const bool binary = true, const int compression_level = Z_DEFAULT_COMPRESSION);

  explicit VariantWriter(const VariantHeader& header, const std::string& output_fname = "-", const bool binary = true, const int compression_level = Z_DEFAULT_COMPRESSION);

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

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

  void add_record(const Variant& body);

  void add_header(const VariantHeader& header);

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

  static htsFile* open_file(const std::string& output_fname, const std::string& binary);
  void write_header() const;
  std::string write_mode(const bool binary, const int compression_level) const;
};

}

#endif // gamgee__variant_writer__guard