source: trunk/test/bam_pair_iterator.cc @ 3201

Last change on this file since 3201 was 3201, checked in by Peter, 8 years ago

add #define YAT_HAVE_LIBBAM to API and replace HAVE_LIBBAM accordingly.

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1// $Id: bam_pair_iterator.cc 3201 2014-05-03 12:57:59Z 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 YAT_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 <algorithm>
31#include <cassert>
32#include <string>
33
34using namespace theplu::yat;
35using namespace omic;
36
37void test1(test::Suite& suite);
38
39int main(int argc, char* argv[])
40{
41  test::Suite suite(argc, argv, true);
42  try {
43    test1(suite);
44  }
45  catch (std::runtime_error& e) {
46    suite.add(false);
47    suite.err() << "error: what: " << e.what() << "\n";
48  }
49  return suite.return_value();
50}
51
52using namespace omic;
53
54void test1(test::Suite& suite)
55{
56#ifdef YAT_HAVE_LIBBAM
57  std::string file = "../../data/foo.sorted.bam";
58
59  InBamFile in(file);
60  BamReadIterator iter(in);
61  BamReadIterator end;
62
63  std::vector<BamPair> result;
64  BamPairIterator<BamReadIterator> piter(iter, end);
65  BamPairIterator<BamReadIterator> pend(end, end);
66  for (; piter!=pend; ++piter) {
67    result.push_back(*piter);
68    result.back() = *piter;
69    // This code doesn't work with boost 1.48 (or older). See
70    // https://svn.boost.org/trac/boost/ticket/5697 for details. It's
71    // not obvious the fix was included in v1.49, but let's test here
72    // and if it wasn't modify this test accordingly and update the
73    // docs in 'yat/omic/BamPairIterator.h'.
74    result.back().first() = piter->first();
75    result.back().second() = piter->second();
76  }
77  // not really doing anything since we've already iterated through
78  // the range, but checking that bam_pair_iterator functions compile
79  std::copy(bam_pair_iterator(iter, end), bam_pair_iterator(end),
80            result.begin());
81
82  in.close();
83  if (!suite.add(result.size()))
84    suite.err() << "error: empty result\n";
85
86  // suite.test_input_iterator(piter);
87#endif
88}
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