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.hpp

/*************************************************************************\
 * AdapterRemoval - cleaning next-generation sequencing reads            *
 *                                                                       *
 * Copyright (C) 2017 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/>. *
\*************************************************************************/
#pragma once

#include "commontypes.hpp" // for string_vec
#include "linereader.hpp"  // for line_reader_base
#include <cstddef>         // for size_t
#include <memory>          // for unique_ptr
#include <string>          // for string

namespace adapterremoval {

/**
 * Multi-file line-reader
 *
 * Wrapper around line_reader that automatically reads through one or more
 * files, returning the content as a contiguous stream of lines. No assumptions
 * are made about the format of the individual files.
 */
class joined_line_readers : public line_reader_base
{
public:
  /** Creates line-reader over multiple files in the specified order. */
  explicit joined_line_readers(const string_vec& filenames);

  /**
   * Reads a line from the currently open file; if EOF is encountered, the
   * currently open file is closed and the next file is opened. Returns true
   * if a line was successfully read, or false if no files remain.
   */
  bool getline(std::string& dst) override;

  /** Currently open file; empty if no file is open. */
  const std::string& filename() const { return m_filename; }

  /** Line number in the current file (1-based); 0 if no file is open. */
  size_t linenumber() const { return m_current_line; }

  joined_line_readers(const joined_line_readers&) = delete;
  joined_line_readers(joined_line_readers&&) = delete;
  joined_line_readers& operator=(const joined_line_readers&) = delete;
  joined_line_readers& operator=(joined_line_readers&&) = delete;

private:
  /**
   * Open the next file, removes it from the queue, and returns true; returns
   * false if no files remain to be processed.
   */
  bool open_next_file();

  //! Files left to read; stored in reverse order.
  string_vec m_filenames{};
  //! Currently open file, if any.
  std::unique_ptr<line_reader> m_reader{};
  //! The currently open file
  std::string m_filename{};
  //! Current line across all files.
  size_t m_current_line = 0;
};

} // namespace adapterremoval

1	/*************************************************************************\
2	* AdapterRemoval - cleaning next-generation sequencing reads *
3	* *
4	* Copyright (C) 2017 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	#pragma once
20
21	#include "commontypes.hpp" // for string_vec
22	#include "linereader.hpp" // for line_reader_base
23	#include <cstddef> // for size_t
24	#include <memory> // for unique_ptr
25	#include <string> // for string
26
27	namespace adapterremoval {
28
29	/**
30	* Multi-file line-reader
31	*
32	* Wrapper around line_reader that automatically reads through one or more
33	* files, returning the content as a contiguous stream of lines. No assumptions
34	* are made about the format of the individual files.
35	*/
36	class joined_line_readers : public line_reader_base
37	{
38	public:
39	/** Creates line-reader over multiple files in the specified order. */
40	explicit joined_line_readers(const string_vec& filenames);
41
42	/**
43	* Reads a line from the currently open file; if EOF is encountered, the
44	* currently open file is closed and the next file is opened. Returns true
45	* if a line was successfully read, or false if no files remain.
46	*/
47	bool getline(std::string& dst) override;
48
49	/** Currently open file; empty if no file is open. */
50	const std::string& filename() const { return m_filename; }	×
51
52	/** Line number in the current file (1-based); 0 if no file is open. */
53	size_t linenumber() const { return m_current_line; }	×
54
55	joined_line_readers(const joined_line_readers&) = delete;
56	joined_line_readers(joined_line_readers&&) = delete;
57	joined_line_readers& operator=(const joined_line_readers&) = delete;
58	joined_line_readers& operator=(joined_line_readers&&) = delete;
59
60	private:
61	/**
62	* Open the next file, removes it from the queue, and returns true; returns
63	* false if no files remain to be processed.
64	*/
65	bool open_next_file();
66
67	//! Files left to read; stored in reverse order.
68	string_vec m_filenames{};
69	//! Currently open file, if any.
70	std::unique_ptr<line_reader> m_reader{};
71	//! The currently open file
72	std::string m_filename{};
73	//! Current line across all files.
74	size_t m_current_line = 0;
75	};
76
77	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #45

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