source: trunk/test/bam_region_iterator.cc @ 2895

Last change on this file since 2895 was 2895, checked in by Peter, 9 years ago

add two tests for bam functionality

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 1.9 KB
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1// $Id: bam_region_iterator.cc 2895 2012-12-10 21:38:12Z peter $
2//
3// Copyright (C) 2012 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#include "yat/omic/BamReadIterator.h"
23#include "yat/omic/BamWriteIterator.h"
24
25#include <bam.h>
26
27#include <algorithm>
28#include <cassert>
29#include <fstream>
30#include <iostream>
31#include <string>
32
33using namespace theplu::yat;
34using namespace theplu::yat::omic;
35
36void test1(test::Suite& suite)
37{
38  std::string file = "../../data/foo.sorted.bam";
39
40  InBamFile bam_stream(file);
41  if (!bam_stream.is_open()) {
42    suite.err() << "cannot read " << file << "\n";
43    suite.add(false);
44    return;
45  }
46  int begin = 24500;
47  int endpos = 24600;
48  BamReadIterator first(bam_stream, 1, begin, endpos);
49  BamReadIterator end;
50
51  int count = 0;
52  while (first != end) {
53    if (!suite.add(first->pos() < endpos) || !suite.add(first->end() > begin))
54      suite.err() << "error: " << first->pos() << "-" << first->end() << "\n";
55    ++count;
56    ++first;
57  }
58  suite.out() << count << std::endl;
59
60  if (count==185)
61    return;
62
63  suite.err() << "count: " << count << "\nexpected: 185\n";
64  suite.add(false);
65}
66
67
68int main(int argc, char* argv[])
69{
70#ifndef HAVE_SAMTOOLS
71  return EXIT_SKIP;
72#endif
73  test::Suite suite(argc, argv);
74
75  try {
76    test1(suite);
77  }
78  catch (std::runtime_error& e) {
79    suite.err() << "what: " << e.what() << "\n";
80    suite.add(false);
81  }
82
83  return suite.return_value();
84}
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