source: trunk/test/cigar_iterator.cc @ 3336

Last change on this file since 3336 was 3336, checked in by Peter, 7 years ago

closes #816

  • Property svn:eol-style set to native
  • Property svn:keywords set to Id
File size: 2.5 KB
Line 
1// $Id: cigar_iterator.cc 3336 2014-10-24 23:27:45Z peter $
2
3/*
4  Copyright (C) 2014 Peter Johansson
5
6  This file is part of the yat library, http://dev.thep.lu.se/yat
7
8  The yat library is free software; you can redistribute it and/or
9  modify it under the terms of the GNU General Public License as
10  published by the Free Software Foundation; either version 3 of the
11  License, or (at your option) any later version.
12
13  The yat library is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16  General Public License for more details.
17
18  You should have received a copy of the GNU General Public License
19  along with yat. If not, see <http://www.gnu.org/licenses/>.
20*/
21
22#include <config.h>
23
24#include "Suite.h"
25
26#include "yat/utility/Cigar.h"
27#include "yat/utility/CigarIterator.h"
28
29#include <boost/cstdint.hpp>
30
31#include <cassert>
32
33using namespace theplu::yat;
34
35void test1(test::Suite& suite);
36
37int main(int argc, char* argv[])
38{
39  test::Suite suite(argc, argv);
40
41  test1(suite);
42
43  return suite.return_value();
44}
45
46void test1(test::Suite& suite)
47{
48  // create a cigar 5S4M1D3M1I4M
49  std::vector<uint32_t> oplen;
50  std::vector<uint32_t> op;
51  oplen.push_back(5);
52  oplen.push_back(4);
53  oplen.push_back(1);
54  oplen.push_back(3);
55  oplen.push_back(1);
56  oplen.push_back(4);
57
58  op.push_back(BAM_CSOFT_CLIP);
59  op.push_back(BAM_CMATCH);
60  op.push_back(BAM_CDEL);
61  op.push_back(BAM_CMATCH);
62  op.push_back(BAM_CINS);
63  op.push_back(BAM_CMATCH);
64
65  assert(oplen.size()==op.size());
66  std::vector<uint32_t> cigar;
67  std::vector<uint32_t> long_cigar;
68  for (size_t i=0; i<op.size(); ++i) {
69    cigar.push_back(bam_cigar_gen(oplen[i], op[i]));
70    for (size_t j=0; j<oplen[i]; ++j)
71      long_cigar.push_back(op[i]);
72  }
73
74  typedef std::vector<uint32_t>::const_iterator Base;
75  utility::CigarIterator<Base> iter(cigar.begin());
76  utility::CigarIterator<Base> end(cigar.end());
77  std::vector<uint32_t>::const_iterator iter2 = long_cigar.begin();
78  while (iter!=end) {
79    assert(iter2<long_cigar.end());
80    if (*iter != *iter2) {
81      suite.add(false);
82      suite.err() << (iter2 - long_cigar.begin()) << " "
83                  << *iter << " " << *iter2 << "\n";
84    }
85    ++iter;
86    ++iter2;
87  }
88
89  utility::CigarIterator<Base> iter3(cigar.begin());
90  utility::CigarIterator<Base> iter4(cigar.begin()+3, 1);
91  std::advance(iter3, oplen[0]+oplen[1]+oplen[2]+1);
92  if (iter3 != iter4) {
93    suite.add(false);
94    suite.err() << "error: iter3!=iter4\n";
95  }
96  // do not run compiler test
97  if (false) {
98    test::test_readable_iterator(iter3);
99    test::test_bidirectional_traversal_iterator(iter3);
100  }
101}
Note: See TracBrowser for help on using the repository browser.