//Copyright 2017 Ryan Wick

//This file is part of Bandage

//Bandage 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.

//Bandage 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 Bandage.  If not, see <http://www.gnu.org/licenses/>.


#ifndef QUERYPATHS_H
#define QUERYPATHS_H


#include <QStringList>
#include "../ui/mainwindow.h"
#include <QTextStream>
#include <QApplication>

int bandageQueryPaths(QStringList arguments);
void printQueryPathsUsage(QTextStream * out, bool all);
QString checkForInvalidQueryPathsOptions(QStringList arguments);
void parseQueryPathsOptions(QStringList arguments, bool *pathFasta,
                            bool * hitsFasta);

#endif // QUERYPATHS_H