// Copyright 2017 Ryan Wick (rrwick@gmail.com)
// https://github.com/rrwick/Unicycler

// This file is part of Unicycler. Unicycler 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. Unicycler 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 Unicycler. If not, see <http://www.gnu.org/licenses/>.

#ifndef START_END_ALIGN_H
#define START_END_ALIGN_H


#include <seqan/sequence.h>

using namespace seqan;

// Functions that are called by the Python script must have C linkage, not C++ linkage.
extern "C" {
    int startAlignment(char * s1, char * s2,
                       int matchScore, int mismatchScore, int gapOpenScore, int gapExtensionScore);
    int endAlignment(char * s1, char * s2,
                     int matchScore, int mismatchScore, int gapOpenScore, int gapExtensionScore);
}

int startEndAlignment(char * s1, char * s2, bool start,
                      int matchScore, int mismatchScore, int gapOpenScore, int gapExtensionScore);

#endif // START_END_ALIGN_H
