/**
 * 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 <U2Core/Task.h>

namespace U2 {
namespace LocalWorkflow {

class StringtieGeneAbundanceReportTask : public Task {
    Q_OBJECT
public:
    StringtieGeneAbundanceReportTask(const QStringList& stringtieReports,
                                     const QString& reportUrl,
                                     const QString& workingDir);

    const QString& getReportUrl() const;
    static const int BUFF_SIZE;
    static const QString inputDelimiter;
    static const QString outputDelimiter;
    static const QString columnName;

private:
    void run();

    const QStringList stringtieReports;
    const QString workingDir;
    QString reportUrl;

    QString sortAndShrinkToTemp(QString tsvFile, QString runDir);
    bool mergeFpkmToReportUrl(QMap<QString, QString> mapFiles, QString reportUrl);
    static QList<QStringList> parseLinesIntoTokens(const QString& text);
};

}  // namespace LocalWorkflow
}  // namespace U2
