source: branches/0.10-stable/test/bam.cc @ 2972

// $Id: bam.cc 2972 2013-01-26 06:53:56Z peter $
//
// Copyright (C) 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/BamFile.h"
#include "yat/omic/BamRead.h"
#endif

#include <cassert>
#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
#ifdef HAVE_LIBBAM
  test1(suite);
#endif
  return suite.return_value();
}

#ifdef HAVE_LIBBAM
using namespace omic;

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

  InBamFile in;
  in.open(file);
  BamRead bam;
  in.read(bam);
  std::string str = "AGCTTTGTTATTATTTGAGGGTGTGGTTCAGTTGTAAACAGTGTATG"
    "TTTTAGAATTTGTGTTATTGTGATGGCGATGACCAAGTACAACATATTTCCCA";
  std::string seq = bam.sequence();
  if (str!=seq) {
    suite.err() << "incorrect sequence: '" << bam.sequence() << "'\n";
    suite.err() << "expected:           '" << str << "'\n";
    suite.add(false);
  }
}
#endif