// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
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// Author: Derek Barnett

#ifndef BAMWRITER_H
#define BAMWRITER_H

#include "pbbam/BamHeader.h"
#include "pbbam/BamRecord.h"
#include "pbbam/Config.h"
#include <htslib/sam.h>
#include <string>

namespace PacBio {
namespace BAM {

class BamFile;

namespace internal { class BamWriterPrivate; }

class PBBAM_EXPORT BamWriter
{
public:
    /// This enum allows you to control the compression level of the output BAM file.
    ///
    /// Values are equivalent to zlib compression levels. See its documentation for more details:
    /// http://www.zlib.net/manual.html
    enum CompressionLevel
    {
        CompressionLevel_0 = 0
      , CompressionLevel_1 = 1
      , CompressionLevel_2 = 2
      , CompressionLevel_3 = 3
      , CompressionLevel_4 = 4
      , CompressionLevel_5 = 5
      , CompressionLevel_6 = 6
      , CompressionLevel_7 = 7
      , CompressionLevel_8 = 8
      , CompressionLevel_9 = 9

      , DefaultCompression = -1
      , NoCompression      = CompressionLevel_0
      , FastCompression    = CompressionLevel_1
      , BestCompression    = CompressionLevel_9
    };

public:

    /// \name Constructors & Related Methods
    /// \{

    /// Opens a BAM file for writing & writes the header information.
    ///
    /// The error status will be set if either operation fails.
    ///
    /// \note Set \p filename to "-" for stdout.
    ///
    /// \param[in] filename         path to output BAM file
    /// \param[in] header           BamHeader object
    /// \param[in] compressionLevel zlib compression level
    /// \param[in] numThreads       number of threads for compression.
    ///            If set to 0, BamWriter will attempt to determine a reasonable estimate.
    ///            If set to 1, this will force single-threaded execution.
    ///            No checks are made against an upper limit.
    BamWriter(const std::string& filename,
              const BamHeader& header,
              const BamWriter::CompressionLevel compressionLevel = BamWriter::DefaultCompression,
              const size_t numThreads = 4);

    /// Fully flushes all buffered data & closes file.
    ~BamWriter(void);

    /// \}

public:

    /// \name Data Writing & Resource Management

    /// Try to flush any buffered data to file.
    ///
    /// \note The underlying implementation doesn't necessarily flush buffered data
    ///       immediately, especially in a multithreaded writer situation.
    ///       Let the BamWriter go out of scope to fully ensure flushing.
    ///
    /// \throws
    void TryFlush(void);

    /// Write a record to the output BAM file.
    ///
    /// \param[in] record BamRecord object
    /// \throws std::runtime_error on failure to write
    void Write(const BamRecord& record);

    /// Write a record to the output BAM file.
    ///
    /// \param[in] record BamRecord object
    /// \param[out] vOffset BGZF virtual offset to start of \p record
    /// \throws std::runtime_error on failure to write
    void Write(const BamRecord& record, int64_t* vOffset);

    /// Write a record to the output BAM file.
    ///
    /// \param[in] recordImpl BamRecordImpl object
    /// \throws std::runtime_error on failure to write
    void Write(const BamRecordImpl& recordImpl);

    /// \}

private:
    std::unique_ptr<internal::BamWriterPrivate> d_;
    DISABLE_MOVE_AND_COPY(BamWriter);
};

} // namespace BAM
} // namespace PacBio

#endif // BAMWRITER_H
