source: trunk/test/bam_pair_analyse.cc @ 3175

// $Id: bam_pair_analyse.cc 3175 2014-03-15 08:15:51Z 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"

using namespace theplu::yat;

#if HAVE_LIBBAM
#include "yat/omic/algorithm.h"
#include "yat/omic/BamRead.h"
#include "yat/omic/BamReadIterator.h"
#endif

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 available\n";
  return EXIT_SKIP;
#endif

#ifdef HAVE_LIBBAM
  test1(suite);
#endif
  return suite.return_value();
}


#ifdef HAVE_LIBBAM
using namespace omic;

class Counter
{
public:
  Counter(void) : n_(0) {}
  void operator()(const BamRead& first, const BamRead& second)
  {
    if (first.core().qual >= 20 && second.core().qual >= 20)
      ++n_;
  }
  int n_;
};

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

  InBamFile is(file);
  BamReadIterator iter(is);
  BamReadIterator end;
  Counter counter;
  bam_pair_analyse(iter, end, counter);
  if (!suite.add(counter.n_==395))
    suite.err() << "n: " << counter.n_ << "; expected 395\n";
  is.close();
}
#endif