MikkelSchubert / adapterremoval / #68

Committed 19 Mar 2025 04:27PM UTC coverage: 27.092% (-0.02%) from 27.114%

Build # #68

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

add default terminate handler (#90)

This allows error handling in the scheduler to be simplified and
simplifies debugging. The auto-generated GDB wrapper scripts are updated
to break on this handler

Run Details

0 of 31 new or added lines in 2 files covered. (0.0%)

5 existing lines in 2 files now uncovered.

2597 of 9586 relevant lines covered (27.09%)

4264.39 hits per line

Source File
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0.0

/src/main.cpp

/*************************************************************************\
 * AdapterRemoval - cleaning next-generation sequencing reads            *
 *                                                                       *
 * Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk            *
 * Copyright (C) 2014 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 "main.hpp"
#include "argparse.hpp"   // for parse_result, parse_result::error, parse_...
#include "debug.hpp"      // for AR_FAIL
#include "logging.hpp"    // for log_stream, error
#include "reports.hpp"    // for print_terminal_postamble, print_terminal_...
#include "userconfig.hpp" // for ar_command, userconfig, ar_command::demul...
#include <cstdlib>        // for abort, size_t
#include <exception>      // for set_terminate
#include <ios>            // for ios_base

namespace adapterremoval {

// See main_adapter_rm.cpp
int
remove_adapter_sequences(const userconfig& config);
// See main_adapter_id.cpp
int
identify_adapter_sequences(const userconfig& config);
// See main_demultiplex.cpp
int
demultiplex_sequences(const userconfig& config);
// See main_fastq_ro.cpp
int
fastq_report_only(const userconfig& config);
// See main_benchmark.cpp
int
benchmark(const userconfig& config);

[[noreturn]] void
terminate(const std::string& message)
{
  log::error()
    << message << "\n"
    << "This should not happen! Please file a bug-report at\n"
    << "    https://github.com/MikkelSchubert/adapterremoval/issues/new\n\n"
    << "Please specify the AdapterRemoval version used (" << VERSION << ")\n"
    << "and if possible describe the steps taken to reproduce this problem.";

  std::abort();
}

[[noreturn]] void
terminate_on_exception()
{
  try {
    std::exception_ptr eptr{ std::current_exception() };

    if (eptr) {
      std::rethrow_exception(eptr);
    } else {
      terminate("Aborted due to unknown error");
    }
  } catch (const std::exception& ex) {
    log::error()
      << ex.what()
      << "\nAdapterRemoval did not run to completion; do NOT make use of the "
         "resulting reads!";
  } catch (...) {
    terminate("Caught unknown exception type");
  }

  std::exit(1);
}

} // namespace adapterremoval

int
main(int argc, char* argv[])
{
  using namespace adapterremoval;

  std::set_terminate(&terminate_on_exception);
  std::ios_base::sync_with_stdio(false);

  userconfig config;

  const std::vector<std::string> argvec(argv, argv + argc);
  switch (config.parse_args(argvec)) {
    case argparse::parse_result::error:
      return 1;

    case argparse::parse_result::exit:
      // --version, --help, or similar used.
      return 0;

    case argparse::parse_result::ok:
      // Ok
      break;

    default:
      AR_FAIL("invalid argparse::parse_result");
  }

  print_terminal_preamble(config);

  auto returncode = 0;
  switch (config.run_type) {
    case ar_command::demultiplex_only:
    case ar_command::trim_adapters: {
      returncode = remove_adapter_sequences(config);
      break;
    }

    case ar_command::benchmark: {
      returncode = benchmark(config);
      break;
    }

    case ar_command::report_only: {
      returncode = identify_adapter_sequences(config);
      break;
    }

    default: {
      log::error() << "Unknown run-type: "
                   << static_cast<size_t>(config.run_type);
      return 1;
    }
  }

  print_terminal_postamble(config, returncode);

  return returncode;
}

1	/*************************************************************************\
2	* AdapterRemoval - cleaning next-generation sequencing reads *
3	* *
4	* Copyright (C) 2011 by Stinus Lindgreen - stinus@binf.ku.dk *
5	* Copyright (C) 2014 by Mikkel Schubert - mikkelsch@gmail.com *
6	* *
7	* This program is free software: you can redistribute it and/or modify *
8	* it under the terms of the GNU General Public License as published by *
9	* the Free Software Foundation, either version 3 of the License, or *
10	* (at your option) any later version. *
11	* *
12	* This program is distributed in the hope that it will be useful, *
13	* but WITHOUT ANY WARRANTY; without even the implied warranty of *
14	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
15	* GNU General Public License for more details. *
16	* *
17	* You should have received a copy of the GNU General Public License *
18	* along with this program. If not, see <http://www.gnu.org/licenses/>. *
19	\*************************************************************************/
20	#include "main.hpp"
21	#include "argparse.hpp" // for parse_result, parse_result::error, parse_...
22	#include "debug.hpp" // for AR_FAIL
23	#include "logging.hpp" // for log_stream, error
24	#include "reports.hpp" // for print_terminal_postamble, print_terminal_...
25	#include "userconfig.hpp" // for ar_command, userconfig, ar_command::demul...
26	#include <cstdlib> // for abort, size_t
27	#include <exception> // for set_terminate
28	#include <ios> // for ios_base
29
30	namespace adapterremoval {
31
32	// See main_adapter_rm.cpp
33	int
34	remove_adapter_sequences(const userconfig& config);
35	// See main_adapter_id.cpp
36	int
37	identify_adapter_sequences(const userconfig& config);
38	// See main_demultiplex.cpp
39	int
40	demultiplex_sequences(const userconfig& config);
41	// See main_fastq_ro.cpp
42	int
43	fastq_report_only(const userconfig& config);
44	// See main_benchmark.cpp
45	int
46	benchmark(const userconfig& config);
47
48	[[noreturn]] void
49	terminate(const std::string& message)	×
50	{
51	log::error()	×
52	<< message << "\n"	×
53	<< "This should not happen! Please file a bug-report at\n"	×
54	<< " https://github.com/MikkelSchubert/adapterremoval/issues/new\n\n"	×
55	<< "Please specify the AdapterRemoval version used (" << VERSION << ")\n"	×
56	<< "and if possible describe the steps taken to reproduce this problem.";	×
57
58	std::abort();	×
59	}
60
61	[[noreturn]] void
NEW 62	terminate_on_exception()	×
63	{
NEW 64	try {	×
NEW 65	std::exception_ptr eptr{ std::current_exception() };	×
66
NEW 67	if (eptr) {	×
NEW 68	std::rethrow_exception(eptr);	×
69	} else {
NEW 70	terminate("Aborted due to unknown error");	×
71	}
NEW 72	} catch (const std::exception& ex) {	×
NEW 73	log::error()	×
NEW 74	<< ex.what()	×
75	<< "\nAdapterRemoval did not run to completion; do NOT make use of the "
NEW 76	"resulting reads!";	×
NEW 77	} catch (...) {	×
NEW 78	terminate("Caught unknown exception type");	×
NEW 79	}	×
80
NEW 81	std::exit(1);	×
82	}
83
84	} // namespace adapterremoval
85
86	int
87	main(int argc, char* argv[])	×
88	{
89	using namespace adapterremoval;	×
90
NEW 91	std::set_terminate(&terminate_on_exception);	×
UNCOV 92	std::ios_base::sync_with_stdio(false);	×
93
94	userconfig config;	×
95
96	const std::vector<std::string> argvec(argv, argv + argc);	×
97	switch (config.parse_args(argvec)) {	×
98	case argparse::parse_result::error:
99	return 1;
100
101	case argparse::parse_result::exit:	×
102	// --version, --help, or similar used.
103	return 0;	×
104
105	case argparse::parse_result::ok:	×
106	// Ok
107	break;	×
108
109	default:	×
110	AR_FAIL("invalid argparse::parse_result");	×
111	}
112
113	print_terminal_preamble(config);	×
114
115	auto returncode = 0;	×
116	switch (config.run_type) {	×
117	case ar_command::demultiplex_only:	×
118	case ar_command::trim_adapters: {	×
119	returncode = remove_adapter_sequences(config);	×
120	break;
121	}
122
123	case ar_command::benchmark: {	×
124	returncode = benchmark(config);	×
125	break;
126	}
127
128	case ar_command::report_only: {	×
129	returncode = identify_adapter_sequences(config);	×
130	break;
131	}
132
133	default: {	×
134	log::error() << "Unknown run-type: "	×
135	<< static_cast<size_t>(config.run_type);	×
136	return 1;	×
137	}
138	}
139
140	print_terminal_postamble(config, returncode);	×
141
142	return returncode;
143	}

MikkelSchubert / adapterremoval / #68

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