/usr/include/pbbam/SamWriter.h is in libpbbam-dev 0.7.4+ds-1build2.
This file is owned by root:root, with mode 0o644.
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//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
//
// File Description
/// \file SamWriter.h
/// \brief Defines the SamWriter class.
//
// Author: Derek Barnett
#ifndef SAMWRITER_H
#define SAMWRITER_H
#include "pbbam/BamHeader.h"
#include "pbbam/BamRecord.h"
#include "pbbam/IRecordWriter.h"
#include <memory>
#include <string>
namespace PacBio {
namespace BAM {
namespace internal { class SamWriterPrivate; }
/// \brief The SamWriter class provides a writing interface for creating
/// new SAM 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 SamWriter is destroyed yields undefined
/// behavior. Enclose the SamWriter 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}
/// {
/// SamWriter w(...);
/// // write data
/// }
/// // now safe to access the new file
/// \endcode
///
///
class SamWriter : public IRecordWriter
{
public:
/// \brief Opens a SAM file for writing & writes the header information.
///
/// \note Set \p filename to "-" for stdout.
///
/// \param[in] filename path to output SAM file
/// \param[in] header BamHeader object
///
/// \throws std::runtime_error if there was a problem opening the file for
/// writing or if an error occurred while writing the header
///
SamWriter(const std::string& filename, const BamHeader& header);
/// Fully flushes all buffered data & closes file.
///
~SamWriter(void);
public:
/// \brief Try to flush any buffered data to file.
///
/// \note The underlying implementation may not necessarily flush buffered
/// data immediately, especially in a multithreaded writer situation.
/// Let the SamWriter go out of scope to fully ensure flushing.
///
/// \throws std::runtime_error if flush fails
///
void TryFlush(void) override;
/// \brief Write a record to the output SAM file.
///
/// \param[in] record BamRecord object
///
/// \throws std::runtime_error on failure to write
///
void Write(const BamRecord& record) override;
/// \brief Write a record to the output SAM file.
///
/// \param[in] recordImpl BamRecordImpl object
///
/// \throws std::runtime_error on failure to write
///
void Write(const BamRecordImpl& recordImpl) override;
private:
std::unique_ptr<internal::SamWriterPrivate> d_;
DISABLE_MOVE_AND_COPY(SamWriter);
};
} // namesapce BAM
} // namespace PacBio
#endif // SAMWRITER_H
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