// Copyright (c) 2014-2015, 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.
//
// File Description
/// \file BamRecord.inl
/// \brief Inline implementations for the BamRecord class.
//
// Author: Derek Barnett

#include "pbbam/BamRecord.h"

namespace PacBio {
namespace BAM {

inline BamRecord BamRecord::Clipped(const BamRecord& input,
                                    const ClipType clipType,
                                    const PacBio::BAM::Position start,
                                    const PacBio::BAM::Position end)
{
    return input.Clipped(clipType, start, end);
}

inline BamRecord BamRecord::Clipped(const ClipType clipType,
                                    const PacBio::BAM::Position start,
                                    const PacBio::BAM::Position end) const
{
    BamRecord result(*this);
    result.Clip(clipType, start, end);
    return result;
}

inline BamRecord BamRecord::Mapped(const BamRecord& input,
                                   const int32_t referenceId,
                                   const Position refStart,
                                   const Strand strand,
                                   const Cigar& cigar,
                                   const uint8_t mappingQuality)
{
    return input.Mapped(referenceId, refStart, strand, cigar, mappingQuality);
}

inline BamRecord BamRecord::Mapped(const int32_t referenceId,
                                   const Position refStart,
                                   const Strand strand,
                                   const Cigar& cigar,
                                   const uint8_t mappingQuality) const
{
    BamRecord result(*this);
    result.Map(referenceId, refStart, strand, cigar, mappingQuality);
    return result;
}

} // namespace BAM
} // namespace PacBio
