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// Copyright (c) 2015, Pacific Biosciences of California, Inc.
//
// 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.
// Author: Derek Barnett
#ifndef BAMFILEMERGER_H
#define BAMFILEMERGER_H
#include <pbbam/DataSet.h>
#include <pbbam/PbiFilter.h>
#include <pbbam/ProgramInfo.h>
#include <string>
#include <vector>
namespace PacBio {
namespace BAM {
namespace common {
class BamFileMerger
{
public:
/// \brief Runs merger on a dataset, applying any supplied filters.
///
/// When this function exits, a merged BAM (and optional PBI) will have been
/// written and closed.
///
/// \param[in] dataset provides input filenames & filters
/// \param[in] outputFilename resulting BAM output
/// \param[in] mergeProgram info about the calling program. Adds a @PG entry to merged header.
/// \param[in] createPbi if true, creates a PBI alongside output BAM
///
/// \throws std::runtime_error if any any errors encountered while reading or writing
///
static void Merge(const PacBio::BAM::DataSet& dataset,
const std::string& outputFilename,
const PacBio::BAM::ProgramInfo& mergeProgram = PacBio::BAM::ProgramInfo(),
bool createPbi = true);
};
} // namespace common
} // namespace BAM
} // namespace PacBio
#include "BamFileMerger.inl"
#endif // BAMFILEMERGER_H
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