source: trunk/test/bam_region_iterator.cc @ 3056

// $Id: bam_region_iterator.cc 3056 2013-06-24 06:37:21Z peter $
//
// Copyright (C) 2012, 2013 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/BamReadIterator.h"
#include "yat/omic/BamWriteIterator.h"
#include "yat/omic/config_bam.h"
#endif

#ifdef YAT_BAM_HEADER
#include YAT_BAM_HEADER
#endif

#include <yat/utility/Exception.h>

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

using namespace theplu::yat;

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.err() << "what: " << e.what() << "\n";
    suite.add(false);
  }

  return suite.return_value();
}

void test1(test::Suite& suite)
{
#ifdef HAVE_LIBBAM
  using namespace omic;
  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) {
    suite.err() << "count: " << count << "\nexpected: 185\n";
    suite.add(false);
  }

  // test negative coordinates trigger exception
  suite.out() << "test negative coordinates\n";
  try {
    BamReadIterator iter(bam_stream, 1, -2, -1);
    suite.add(false);
    suite.err() << "error: no exception thrown\n";
  }
  catch (utility::runtime_error& e) {
    suite.out() << "expected exception caught with what(): '" << e.what()
                << "'\n";
  }

#endif
}