source: trunk/test/cigar_iterator.cc @ 3336

// $Id: cigar_iterator.cc 3336 2014-10-24 23:27:45Z 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/Cigar.h"
#include "yat/utility/CigarIterator.h"

#include <boost/cstdint.hpp>

#include <cassert>

using namespace theplu::yat;

void test1(test::Suite& suite);

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

  test1(suite);

  return suite.return_value();
}

void test1(test::Suite& suite)
{
  // create a cigar 5S4M1D3M1I4M
  std::vector<uint32_t> oplen;
  std::vector<uint32_t> op;
  oplen.push_back(5);
  oplen.push_back(4);
  oplen.push_back(1);
  oplen.push_back(3);
  oplen.push_back(1);
  oplen.push_back(4);

  op.push_back(BAM_CSOFT_CLIP);
  op.push_back(BAM_CMATCH);
  op.push_back(BAM_CDEL);
  op.push_back(BAM_CMATCH);
  op.push_back(BAM_CINS);
  op.push_back(BAM_CMATCH);

  assert(oplen.size()==op.size());
  std::vector<uint32_t> cigar;
  std::vector<uint32_t> long_cigar;
  for (size_t i=0; i<op.size(); ++i) {
    cigar.push_back(bam_cigar_gen(oplen[i], op[i]));
    for (size_t j=0; j<oplen[i]; ++j)
      long_cigar.push_back(op[i]);
  }

  typedef std::vector<uint32_t>::const_iterator Base;
  utility::CigarIterator<Base> iter(cigar.begin());
  utility::CigarIterator<Base> end(cigar.end());
  std::vector<uint32_t>::const_iterator iter2 = long_cigar.begin();
  while (iter!=end) {
    assert(iter2<long_cigar.end());
    if (*iter != *iter2) {
      suite.add(false);
      suite.err() << (iter2 - long_cigar.begin()) << " "
                  << *iter << " " << *iter2 << "\n";
    }
    ++iter;
    ++iter2;
  }

  utility::CigarIterator<Base> iter3(cigar.begin());
  utility::CigarIterator<Base> iter4(cigar.begin()+3, 1);
  std::advance(iter3, oplen[0]+oplen[1]+oplen[2]+1);
  if (iter3 != iter4) {
    suite.add(false);
    suite.err() << "error: iter3!=iter4\n";
  }
  // do not run compiler test
  if (false) {
    test::test_readable_iterator(iter3);
    test::test_bidirectional_traversal_iterator(iter3);
  }
}