/*
    libmaus2
    Copyright (C) 2009-2013 German Tischler
    Copyright (C) 2011-2013 Genome Research Limited

    This program 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.

    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
*/
#if ! defined(LIBMAUS2_BAMBAM_DUPSETCALLBACK_HPP)
#define LIBMAUS2_BAMBAM_DUPSETCALLBACK_HPP

#include <libmaus2/bambam/ReadEnds.hpp>

namespace libmaus2
{
	namespace bambam
	{
		struct DupSetCallback
		{
			virtual ~DupSetCallback() {}
			virtual void operator()(::libmaus2::bambam::ReadEnds const & A) = 0;
			virtual uint64_t getNumDups() const = 0;
			virtual void addOpticalDuplicates(uint64_t const libid, uint64_t const count) = 0;
			virtual bool isMarked(uint64_t const i) const = 0;
			virtual void flush(uint64_t const n) = 0;
		};
	}
}
#endif
