source: trunk/test/bam_pair_iterator.cc @ 3196

// $Id: bam_pair_iterator.cc 3196 2014-04-22 09:56:17Z peter $
//
// Copyright (C) 2014 Peter Johansson
//
// This program 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.
//
// This program 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 this program. If not, see <http://www.gnu.org/licenses/>.

#include <config.h>

#include "Suite.h"

#ifdef HAVE_LIBBAM
#include "yat/omic/BamFile.h"
#include "yat/omic/BamPairIterator.h"
#include "yat/omic/BamRead.h"
#include "yat/omic/BamReadIterator.h"
#include "yat/omic/BamWriteIterator.h"
#endif

#include <boost/version.hpp>

#include <algorithm>
#include <cassert>
#include <string>

using namespace theplu::yat;
using namespace omic;

void test1(test::Suite& suite);

int main(int argc, char* argv[])
{
  test::Suite suite(argc, argv);
#ifndef HAVE_LIBBAM
  suite.out() << "no libbam\n";
  return EXIT_SKIP;
#endif
#ifndef HAVE_SAMTOOLS
  suite.out() << "no samtools\n";
  return EXIT_SKIP;
#endif
  try {
    test1(suite);
  }
  catch (std::runtime_error& e) {
    suite.add(false);
    suite.err() << "error: what: " << e.what() << "\n";
  }
  return suite.return_value();
}

#ifdef HAVE_LIBBAM
using namespace omic;

void test1(test::Suite& suite)
{
  std::string file = "../../data/foo.sorted.bam";

  InBamFile in(file);
  BamReadIterator iter(in);
  BamReadIterator end;

  std::vector<BamPair> result;
  BamPairIterator<BamReadIterator> piter(iter, end);
  BamPairIterator<BamReadIterator> pend(end, end);
  for (; piter!=pend; ++piter) {
    result.push_back(*piter);
    // This code doesn't work with boost 1.48 (or older). See
    // https://svn.boost.org/trac/boost/ticket/5697 for details. It's
    // not obvious the fix was included in v1.49, but let's test here
    // and if it wasn't modify this test accordingly and update the
    // docs in 'yat/omic/BamPairIterator.h'.
#if BOOST_VERSION > 104800
    result.back().first() = piter->first();
    result.back().second() = piter->second();
#endif
  }
  // not really doing anything since we've already iterated through
  // the range, but checking that bam_pair_iterator functions compile
  std::copy(bam_pair_iterator(iter, end), bam_pair_iterator(end),
            result.begin());

  in.close();
  if (!suite.add(result.size()))
    suite.err() << "error: empty result\n";

  // suite.test_input_iterator(piter);
}
#endif