source: trunk/test/smith_waterman.cc @ 3209

// $Id: smith_waterman.cc 3209 2014-05-04 13:52:34Z peter $

/*
  Copyright (C) 2014 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library 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.

  The yat library 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 yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include <config.h>

#include "Suite.h"

#include "yat/utility/Matrix.h"
#include "yat/utility/SmithWaterman.h"

using namespace theplu::yat;

int main(int argc, char* argv[])
{
  test::Suite suite(argc, argv);

  std::string ref = "XXXXXABCDEFGHIJDKLMNOPQRSTUVWXYZABCDEFGHXXXXXXXXXXXXXXX";
  std::string seq =    "SSABCDEFGHIJKLMNOPQRSTUIVWXYZxBCDEFGHS";

  suite.out() << "ref: " << ref << "\n";
  suite.out() << "seq: " << seq << "\n";

  utility::SmithWaterman sw(2,3);
  double score = sw(ref.begin(), ref.end(), seq.begin(), seq.end(), 3);
  suite.out() << "sw score: " << score << "\n";

  utility::Aligner::Cigar cig = sw.cigar();
  std::ostringstream os;
  os << cig;
  suite.out() << os.str() << "\n";
  std::string str = "2S10=1D11=1I5=1X7=1S";
  if (os.str()!=str) {
    suite.add(false);
    suite.err() << "error: incorrect CIGAR string, expected\n" << str << "\n";
  }

  suite.out() << "pos: " << sw.position() << "\n";
  if (sw.position()!=5)
    suite.err() << "error: wrong position: " << sw.position()
                << " expected 4\n";

  utility::Matrix x = sw.score();
  return suite.return_value();
}