source: trunk/test/bam_pair_iterator.cc @ 3196

Last change on this file since 3196 was 3196, checked in by Peter, 8 years ago

avoid test code that won't compile with old boost.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 2.6 KB
Line 
1// $Id: bam_pair_iterator.cc 3196 2014-04-22 09:56:17Z peter $
2//
3// Copyright (C) 2014 Peter Johansson
4//
5// This program is free software; you can redistribute it and/or modify
6// it under the terms of the GNU General Public License as published by
7// the Free Software Foundation; either version 3 of the License, or
8// (at your option) any later version.
9//
10// This program is distributed in the hope that it will be useful, but
11// WITHOUT ANY WARRANTY; without even the implied warranty of
12// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
13// General Public License for more details.
14//
15// You should have received a copy of the GNU General Public License
16// along with this program. If not, see <http://www.gnu.org/licenses/>.
17
18#include <config.h>
19
20#include "Suite.h"
21
22#ifdef HAVE_LIBBAM
23#include "yat/omic/BamFile.h"
24#include "yat/omic/BamPairIterator.h"
25#include "yat/omic/BamRead.h"
26#include "yat/omic/BamReadIterator.h"
27#include "yat/omic/BamWriteIterator.h"
28#endif
29
30#include <boost/version.hpp>
31
32#include <algorithm>
33#include <cassert>
34#include <string>
35
36using namespace theplu::yat;
37using namespace omic;
38
39void test1(test::Suite& suite);
40
41int main(int argc, char* argv[])
42{
43  test::Suite suite(argc, argv);
44#ifndef HAVE_LIBBAM
45  suite.out() << "no libbam\n";
46  return EXIT_SKIP;
47#endif
48#ifndef HAVE_SAMTOOLS
49  suite.out() << "no samtools\n";
50  return EXIT_SKIP;
51#endif
52  try {
53    test1(suite);
54  }
55  catch (std::runtime_error& e) {
56    suite.add(false);
57    suite.err() << "error: what: " << e.what() << "\n";
58  }
59  return suite.return_value();
60}
61
62#ifdef HAVE_LIBBAM
63using namespace omic;
64
65void test1(test::Suite& suite)
66{
67  std::string file = "../../data/foo.sorted.bam";
68
69  InBamFile in(file);
70  BamReadIterator iter(in);
71  BamReadIterator end;
72
73  std::vector<BamPair> result;
74  BamPairIterator<BamReadIterator> piter(iter, end);
75  BamPairIterator<BamReadIterator> pend(end, end);
76  for (; piter!=pend; ++piter) {
77    result.push_back(*piter);
78    // This code doesn't work with boost 1.48 (or older). See
79    // https://svn.boost.org/trac/boost/ticket/5697 for details. It's
80    // not obvious the fix was included in v1.49, but let's test here
81    // and if it wasn't modify this test accordingly and update the
82    // docs in 'yat/omic/BamPairIterator.h'.
83#if BOOST_VERSION > 104800
84    result.back().first() = piter->first();
85    result.back().second() = piter->second();
86#endif
87  }
88  // not really doing anything since we've already iterated through
89  // the range, but checking that bam_pair_iterator functions compile
90  std::copy(bam_pair_iterator(iter, end), bam_pair_iterator(end),
91            result.begin());
92
93  in.close();
94  if (!suite.add(result.size()))
95    suite.err() << "error: empty result\n";
96
97  // suite.test_input_iterator(piter);
98}
99#endif
Note: See TracBrowser for help on using the repository browser.