MikkelSchubert / adapterremoval / #45

Committed 20 Sep 2024 06:49PM UTC coverage: 26.244% (-49.2%) from 75.443%

Build # #45

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

attempt to fix coveralls run

Run Details

2458 of 9366 relevant lines covered (26.24%)

4362.23 hits per line

Source File
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0.0

/src/linereader_joined.cpp

/*************************************************************************\
 * AdapterRemoval - cleaning next-generation sequencing reads            *
 *                                                                       *
 * Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com           *
 *                                                                       *
 * 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 "linereader_joined.hpp"
#include <memory> // for make_unique
#include <vector> // for vector

namespace adapterremoval {

joined_line_readers::joined_line_readers(const string_vec& filenames)
  : m_filenames(filenames.rbegin(), filenames.rend())
{
}

bool
joined_line_readers::getline(std::string& dst)
{
  while (true) {
    if (m_reader && m_reader->getline(dst)) {
      m_current_line++;
      return true;
    } else if (!open_next_file()) {
      return false;
    }
  }
}

bool
joined_line_readers::open_next_file()
{
  if (m_filenames.empty()) {
    m_reader.reset();
    return false;
  }

  m_reader = std::make_unique<line_reader>(m_filenames.back());
  m_filename = m_filenames.back();
  m_current_line = 1;

  m_filenames.pop_back();

  return true;
}

} // namespace adapterremoval

1	/*************************************************************************\
2	* AdapterRemoval - cleaning next-generation sequencing reads *
3	* *
4	* Copyright (C) 2015 by Mikkel Schubert - mikkelsch@gmail.com *
5	* *
6	* This program is free software: you can redistribute it and/or modify *
7	* it under the terms of the GNU General Public License as published by *
8	* the Free Software Foundation, either version 3 of the License, or *
9	* (at your option) any later version. *
10	* *
11	* This program is distributed in the hope that it will be useful, *
12	* but WITHOUT ANY WARRANTY; without even the implied warranty of *
13	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
14	* GNU General Public License for more details. *
15	* *
16	* You should have received a copy of the GNU General Public License *
17	* along with this program. If not, see <http://www.gnu.org/licenses/>. *
18	\*************************************************************************/
19	#include "linereader_joined.hpp"
20	#include <memory> // for make_unique
21	#include <vector> // for vector
22
23	namespace adapterremoval {
24
25	joined_line_readers::joined_line_readers(const string_vec& filenames)	×
26	: m_filenames(filenames.rbegin(), filenames.rend())	×
27	{
28	}
29
30	bool
31	joined_line_readers::getline(std::string& dst)	×
32	{
33	while (true) {	×
34	if (m_reader && m_reader->getline(dst)) {	×
35	m_current_line++;	×
36	return true;	×
37	} else if (!open_next_file()) {	×
38	return false;
39	}
40	}
41	}
42
43	bool
44	joined_line_readers::open_next_file()	×
45	{
46	if (m_filenames.empty()) {	×
47	m_reader.reset();	×
48	return false;	×
49	}
50
51	m_reader = std::make_unique<line_reader>(m_filenames.back());	×
52	m_filename = m_filenames.back();	×
53	m_current_line = 1;	×
54
55	m_filenames.pop_back();	×
56
57	return true;	×
58	}
59
60	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #45

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