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

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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 <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();
}

} // namespace adapterremoval

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

  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 <ios> // for ios_base
28
29	namespace adapterremoval {
30
31	// See main_adapter_rm.cpp
32	int
33	remove_adapter_sequences(const userconfig& config);
34	// See main_adapter_id.cpp
35	int
36	identify_adapter_sequences(const userconfig& config);
37	// See main_demultiplex.cpp
38	int
39	demultiplex_sequences(const userconfig& config);
40	// See main_fastq_ro.cpp
41	int
42	fastq_report_only(const userconfig& config);
43	// See main_benchmark.cpp
44	int
45	benchmark(const userconfig& config);
46
47	[[noreturn]] void
48	terminate(const std::string& message)	×
49	{
50	log::error()	×
51	<< message << "\n"	×
52	<< "This should not happen! Please file a bug-report at\n"	×
53	<< " https://github.com/MikkelSchubert/adapterremoval/issues/new\n\n"	×
54	<< "Please specify the AdapterRemoval version used (" << VERSION << ")\n"	×
55	<< "and if possible describe the steps taken to reproduce this problem.";	×
56
57	std::abort();	×
58	}
59
60	} // namespace adapterremoval
61
62	int
63	main(int argc, char* argv[])	×
64	{
65	using namespace adapterremoval;	×
66
67	std::ios_base::sync_with_stdio(false);	×
68
69	userconfig config;	×
70
71	const std::vector<std::string> argvec(argv, argv + argc);	×
72	switch (config.parse_args(argvec)) {	×
73	case argparse::parse_result::error:
74	return 1;
75
76	case argparse::parse_result::exit:	×
77	// --version, --help, or similar used.
78	return 0;	×
79
80	case argparse::parse_result::ok:	×
81	// Ok
82	break;	×
83
84	default:	×
85	AR_FAIL("invalid argparse::parse_result");	×
86	}
87
88	print_terminal_preamble(config);	×
89
90	auto returncode = 0;	×
91	switch (config.run_type) {	×
92	case ar_command::demultiplex_only:	×
93	case ar_command::trim_adapters: {	×
94	returncode = remove_adapter_sequences(config);	×
95	break;
96	}
97
98	case ar_command::benchmark: {	×
99	returncode = benchmark(config);	×
100	break;
101	}
102
103	case ar_command::report_only: {	×
104	returncode = identify_adapter_sequences(config);	×
105	break;
106	}
107
108	default: {	×
109	log::error() << "Unknown run-type: "	×
110	<< static_cast<size_t>(config.run_type);	×
111	return 1;	×
112	}
113	}
114
115	print_terminal_postamble(config, returncode);	×
116
117	return returncode;
118	}

MikkelSchubert / adapterremoval / #45

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