source: trunk/test/bam_region_iterator.cc @ 2895

// $Id: bam_region_iterator.cc 2895 2012-12-10 21:38:12Z peter $
//
// Copyright (C) 2012 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"

#include "yat/omic/BamReadIterator.h"
#include "yat/omic/BamWriteIterator.h"

#include <bam.h>

#include <algorithm>
#include <cassert>
#include <fstream>
#include <iostream>
#include <string>

using namespace theplu::yat;
using namespace theplu::yat::omic;

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

  InBamFile bam_stream(file);
  if (!bam_stream.is_open()) {
    suite.err() << "cannot read " << file << "\n";
    suite.add(false);
    return;
  }
  int begin = 24500;
  int endpos = 24600;
  BamReadIterator first(bam_stream, 1, begin, endpos);
  BamReadIterator end;

  int count = 0;
  while (first != end) {
    if (!suite.add(first->pos() < endpos) || !suite.add(first->end() > begin))
      suite.err() << "error: " << first->pos() << "-" << first->end() << "\n";
    ++count;
    ++first;
  }
  suite.out() << count << std::endl;

  if (count==185)
    return;

  suite.err() << "count: " << count << "\nexpected: 185\n";
  suite.add(false);
}


int main(int argc, char* argv[])
{
#ifndef HAVE_SAMTOOLS
  return EXIT_SKIP;
#endif
  test::Suite suite(argc, argv);

  try {
    test1(suite);
  }
  catch (std::runtime_error& e) {
    suite.err() << "what: " << e.what() << "\n";
    suite.add(false);
  }

  return suite.return_value();
}