MikkelSchubert / adapterremoval / #46

Committed 27 Nov 2024 03:10PM UTC coverage: 27.245% (+1.0%) from 26.244%

Build # #46

Build Type

push

travis-ci

Committed by

MikkelSchubert

Commit Message

fix convenience executable make target

Run Details

2609 of 9576 relevant lines covered (27.25%)

4268.73 hits per line

Source File
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0.0

/src/errors.cpp

/*************************************************************************\
 * AdapterRemoval - cleaning next-generation sequencing reads            *
 *                                                                       *
 * Copyright (C) 2024 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 "errors.hpp" // declarations
#include <array>      // for array
#include <cerrno>     // for errno
#include <cstdio>     // for sys_errlist, sys_nerr
#include <cstring>    // for strerror_r
#include <sstream>    // for operator<<, basic_ostream
#include <string>     // for string

namespace adapterremoval {

// The function signature of strerror_r depends on the libc used. Rather than
// attempting to match defines, simply select the appropriate wrapper based on
// the signature of the function
using glibc_strerror_r = char* (*)(int, char*, size_t);
using posix_strerror_r = int (*)(int, char*, size_t);
//! Recommended buffer size according to `strerror` man page
using strerror_buf = std::array<char, 1024>;

std::string
strerror_r_wrapper(glibc_strerror_r f, int error_number)
{
  strerror_buf buf{};
  return f(error_number, buf.data(), buf.size());
}

std::string
strerror_r_wrapper(posix_strerror_r f, int error_number)
{
  strerror_buf buf{};
  if (f(error_number, buf.data(), buf.size())) {
    return "unknown error " + std::to_string(error_number);
  }

  return buf.data();
}

std::string
format_io_error(const std::string& message, const int error_number)
{
  if (error_number) {
    std::ostringstream stream;
    stream << message << " ('" << strerror_r_wrapper(::strerror_r, error_number)
           << "')";

    return stream.str();
  } else {
    return message;
  }
}

} // namespace adapterremoval

1	/*************************************************************************\
2	* AdapterRemoval - cleaning next-generation sequencing reads *
3	* *
4	* Copyright (C) 2024 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
20	#include "errors.hpp" // declarations
21	#include <array> // for array
22	#include <cerrno> // for errno
23	#include <cstdio> // for sys_errlist, sys_nerr
24	#include <cstring> // for strerror_r
25	#include <sstream> // for operator<<, basic_ostream
26	#include <string> // for string
27
28	namespace adapterremoval {
29
30	// The function signature of strerror_r depends on the libc used. Rather than
31	// attempting to match defines, simply select the appropriate wrapper based on
32	// the signature of the function
33	using glibc_strerror_r = char* ()(int, char, size_t);
34	using posix_strerror_r = int ()(int, char, size_t);
35	//! Recommended buffer size according to `strerror` man page
36	using strerror_buf = std::array<char, 1024>;
37
38	std::string
39	strerror_r_wrapper(glibc_strerror_r f, int error_number)	×
40	{
41	strerror_buf buf{};	×
42	return f(error_number, buf.data(), buf.size());	×
43	}
44
45	std::string
46	strerror_r_wrapper(posix_strerror_r f, int error_number)	×
47	{
48	strerror_buf buf{};	×
49	if (f(error_number, buf.data(), buf.size())) {	×
50	return "unknown error " + std::to_string(error_number);	×
51	}
52
53	return buf.data();	×
54	}
55
56	std::string
57	format_io_error(const std::string& message, const int error_number)	×
58	{
59	if (error_number) {	×
60	std::ostringstream stream;	×
61	stream << message << " ('" << strerror_r_wrapper(::strerror_r, error_number)	×
62	<< "')";	×
63
64	return stream.str();	×
65	} else {	×
66	return message;	×
67	}
68	}
69
70	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #46

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