source: trunk/test/cigar2.cc @ 3342

// $Id: cigar2.cc 3342 2014-11-06 05:26:24Z 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/SmithWaterman.h"

#include <string>
#include <sstream>

using namespace theplu::yat;

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

  std::string ref("AAAGACTTACGATGAGGTCTGGCACCCTGAGCAGTCCAGCGAGGACTTGGTCTTAGTTGAGCAATTTGGCTAGGAGGATA");
  utility::SmithWaterman aligner(2,5);

  std::string query = ref.substr(0, 20);
  double score = aligner(ref.begin(), ref.end(), query.begin(), query.end(),3);
  suite.out() << "score: " << score << "\n";

  query = "ATATTTTGGAATGGATGAGGTCTGGCACCCTGAGCAGTCCAGCGAGGACTTGGTCTTAGCTGAGCAATTTGG";
  score = aligner(ref.begin(), ref.end(), query.begin(), query.end(),3);
  suite.out() << "score: " << score << "\n";

  std::ostringstream os;
  os << aligner.cigar();
  std::string correct("13S46=1X12=");
  if (os.str() != correct) {
    suite.add(false);
    suite.err() << "incorrect cigar: " << aligner.cigar() << "\n";
    suite.err() << "expected: " << correct << "\n";
  }

  return suite.return_value();
}