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#ifndef THIRD_PARTY_NUCLEUS_IO_SAM_WRITER_H_
#define THIRD_PARTY_NUCLEUS_IO_SAM_WRITER_H_

#include <memory>
#include <string>

#include "htslib/hts.h"
#include "htslib/sam.h"
#include "third_party/nucleus/platform/types.h"
#include "third_party/nucleus/protos/reads.pb.h"
#include "third_party/nucleus/util/proto_ptr.h"
#include "third_party/nucleus/core/status.h"
#include "third_party/nucleus/core/statusor.h"

namespace nucleus {

// A SAM/BAM/CRAM writer.
//
// SAM/BAM/CRAM files store information about a biological sequence and its
// corresponding quality scores.
//
// https://samtools.github.io/hts-specs/SAMv1.pdf
// https://samtools.github.io/hts-specs/CRAMv3.pdf
// This class converts nucleus.genomics.v1.SamHeader and
// nucleus.genomics.v1.Read to a file based on the file path passed in.
//
// This uses the htslib C API for writing NGS reads (BAM, SAM, SAM). For details
// of the API, see:
// https://github.com/samtools/htslib/tree/develop/htslib
//
class SamWriter {
 public:
  // Creates a new SamWriter writing to the file at |sam_path|, which is
  // opened and created if needed. Returns either a unique_ptr to the
  // SamWriter or a Status indicating why an error occurred.
  static StatusOr<std::unique_ptr<SamWriter>> ToFile(
      const string& sam_path,
      const nucleus::genomics::v1::SamHeader& sam_header);

  // Creates a new SamWriter writing to the file at |sam_path|, which is
  // opened and created if needed. |ref_path|, which points to an external
  // reference FASTA file, cannot be empty for CRAM files. If |embed_ref|, the
  // CRAM output file will embed the references in the output file. Returns
  // either a unique_ptr to the SamWriter or a Status indicating why an error
  // occurred.
  static StatusOr<std::unique_ptr<SamWriter>> ToFile(
      const string& sam_path, const string& ref_path, bool embed_ref,
      const nucleus::genomics::v1::SamHeader& sam_header);

  ~SamWriter();

  // Disable copy and assignment operations.
  SamWriter(const SamWriter& other) = delete;
  SamWriter& operator=(const SamWriter&) = delete;

  // Write a Read to the  file.
  // Returns Status::OK() if the write was successful; otherwise the status
  // provides information about what error occurred.
  ::nucleus::Status Write(const nucleus::genomics::v1::Read& read);
  ::nucleus::Status WritePython(
      const ConstProtoPtr<const nucleus::genomics::v1::Read>& wrapped) {
    return Write(*(wrapped.p_));
  }

  // Close the underlying resource descriptors. Returns Status::OK() if the
  // close was successful; otherwise the status provides information about what
  // error occurred.
  ::nucleus::Status Close();

  // This no-op function is needed only for Python context manager support. Do
  // not use it!
  void PythonEnter() const {}

 private:
  class NativeHeader;
  class NativeFile;
  class NativeBody;
  // Private constructor; use ToFile to safely create a SamWriter.
  SamWriter(std::unique_ptr<NativeFile> file,
            std::unique_ptr<NativeHeader> header);

  // A pointer to the htslib file used to access the SAM/BAM/CRAM data.
  std::unique_ptr<NativeFile> native_file_;

  // A htslib header data structure obtained by parsing the header of this file.
  std::unique_ptr<NativeHeader> native_header_;
};

}  // namespace nucleus

#endif  // THIRD_PARTY_NUCLEUS_IO_SAM_WRITER_H_