libpbbam-dev 0.7.4+ds-1 / usr / include / pbbam / BamWriter.h

// Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
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// File Description
/// \file BamWriter.h
/// \brief Defines the BamWriter class.
//
// Author: Derek Barnett

#ifndef BAMWRITER_H
#define BAMWRITER_H

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

namespace PacBio {
namespace BAM {

class BamFile;

namespace internal { class BamWriterPrivate; }

/// \brief The BamWriter class provides a writing interface for creating
///        new %BAM files.
///
/// \note The underlying buffered data may not be flushed to the file until the
///       destructor is called. Trying to access the file (reading, stat-ing,
///       indexing, etc.) before the BamWriter is destroyed yields undefined
///       behavior. Enclose the BamWriter in some form of local scope (curly
///       braces, a separate function, etc.) to ensure that its destructor is
///       called before proceeding to read-based operations.
///
/// \code{.cpp}
///  {
///     BamWriter w(...);
///     // write data
///  }
///  // now safe to access the new file
/// \endcode
///
///
class PBBAM_EXPORT BamWriter : public IRecordWriter
{
public:
    /// \brief 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
    };

    /// \brief This enum allows you to control whether BAI bin numbers are
    ///        calculated for output records.
    /// 
    /// For most cases, the default behavior (ON) should be retained for maximum
    /// compatibility with downstream tools (e.g. samtools index). Disabling bin
    /// calculation should only be used if all records are known to never be
    /// mapped, and even then only if profiling revelas the calculation to
    /// affect extremely performance-sensitive, "critical paths".
    ///
    enum BinCalculationMode
    {
        BinCalculation_ON = 0
      , BinCalculation_OFF
    };

public:

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

    /// \brief 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.
    ///
    /// \param[in] binCalculationMode BAI bin calculation mode. The default
    ///            behavior will ensure proper bin numbers are provided for all
    ///            records written. This extra step may turned off when bin
    ///            numbers are not needed. Though if in doubt, keep the default.
    ///
    /// \throws std::runtmie_error if there was a problem opening the file for
    ///         writing or if an error occurred while writing the header
    ///
    BamWriter(const std::string& filename,
              const BamHeader& header,
              const BamWriter::CompressionLevel compressionLevel = BamWriter::DefaultCompression,
              const size_t numThreads = 4,
              const BinCalculationMode binCalculationMode = BamWriter::BinCalculation_ON);

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

    /// \}

public:

    /// \name Data Writing & Resource Management
    /// \{

    /// \brief 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 std::runtime_error if flush fails
    ///
    void TryFlush(void);

    /// \brief 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);

    /// \brief 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);

    /// \brief 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