BamPairBuffer.h

#ifndef _theplu_yat_omic_bam_pair_buffer_
#define _theplu_yat_omic_bam_pair_buffer_

// $Id: BamPairBuffer.h 4057 2021-03-31 05:46:00Z peter $

/*
  Copyright (C) 2021 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License as
  published by the Free Software Foundation; either version 3 of the
  License, or (at your option) any later version.

  The yat library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include "BamRead.h"

#include <yat/utility/SortedBuffer.h>
#include <yat/utility/yat_assert.h>

namespace theplu {
namespace yat {
namespace omic {

  template<typename OutputIterator>
  class BamPairBuffer
  {
  public:
    BamPairBuffer(OutputIterator out)
      : buffer_(out) {}

    void push(const BamRead& first, const BamRead& second)
    {
      // first <= second within each pair
      YAT_ASSERT(BamLessPos()(second, first) == false);
      // read pairs come sorted wrt first, i.e., all future ::first
      // are greater (or equal) than current first, and thus all
      // future reads are greater (or equal) than first.
      buffer_.flush(first);
      buffer_.push(first);
      buffer_.push(second);
    }
  private:
    utility::SortedBuffer<BamRead, OutputIterator, BamLessPos> buffer_;
  };

}}}
#endif