/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2023 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * 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 2
 * 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, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#pragma once

#include <3rdparty/zlib/zlib.h>

#include <U2Core/IOAdapter.h>

#include "VirtualOffset.h"

namespace U2 {
namespace BAM {

class BgzfWriter {
public:
    BgzfWriter(IOAdapter& ioAdapter);
    ~BgzfWriter();

    void write(const char* buff, qint64 size);
    void finish();

    VirtualOffset getOffset() const;

private:
    void finishBlock();

    static const int BUFFER_SIZE = 16384;
    static const int BLOCK_SIZE = 65536;
    IOAdapter& ioAdapter;
    z_stream stream;
    char buffer[BUFFER_SIZE];
    quint64 headerOffset;
    bool blockEnd;
    bool finished;
};

}  // namespace BAM
}  // namespace U2
