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

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web-flow

Commit Message

attempt to fix coveralls run

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0.0

/src/reports_terminal.cpp

/*************************************************************************\
 * AdapterRemoval - cleaning next-generation sequencing reads            *
 *                                                                       *
 * Copyright (C) 2022 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 "commontypes.hpp" // for trimming_strategy, trimming_strategy::mott
#include "debug.hpp"       // for AR_FAIL
#include "logging.hpp"     // for info, log_stream, error, warn
#include "reports.hpp"     // for print_terminal_postamble, print_terminal_...
#include "simd.hpp"        // for name, instruction_set, instruction_set::none
#include "userconfig.hpp"  // for userconfig, ar_command, ar_command::demul...
#include <string>          // for string

namespace adapterremoval {

void
print_trimming_parameters(const userconfig& config)
{
  switch (config.trim) {
    case trimming_strategy::mott:
      log::info() << "  - Mott based quality based trimming with max "
                  << "error-rate " << config.trim_mott_rate;
      break;
    case trimming_strategy::window:
      log::info() << "  - Window based quality based trimming with window size "
                  << config.trim_window_length << "and minimum quality score "
                  << config.trim_quality_score
                  << (config.trim_ambiguous_bases ? " (including Ns)" : "");
      break;
    case trimming_strategy::per_base:
      if (config.trim_low_quality_bases) {
        log::info() << "  - Per-base based quality based trimming with minimum "
                    << "quality score " << config.trim_quality_score
                    << (config.trim_ambiguous_bases ? " (including Ns)" : "");
      } else if (config.trim_ambiguous_bases) {
        log::info() << "  - Per-base based trimming of Ns";
      } else {
        AR_FAIL("this should not be possible");
      }
      break;
    case trimming_strategy::none:
      log::info() << "  - Quality based trimming disabled";
      break;

    default:
      AR_FAIL("not implemented");
  }
}

void
print_terminal_preamble(const userconfig& config)
{
  log::log_preamble();

  if (config.simd == simd::instruction_set::none) {
    log::warn() << "Hardware accelerated alignments disabled!";
  } else {
    log::info() << "Using " << simd::name(config.simd)
                << " accelerated alignments";
  }

  switch (config.run_type) {
    case ar_command::trim_adapters:
      if (config.paired_ended_mode) {
        log::info() << "Trimming adapters from PE reads:";
      } else {
        log::info() << "Trimming adapters from SE reads:";
      }

      print_trimming_parameters(config);
      break;
    case ar_command::benchmark:
      log::info() << "Benchmarking sub-systems";
      break;
    case ar_command::demultiplex_only:
      log::info() << "Demultiplexing reads";
      break;
    case ar_command::report_only:
      log::info() << "Generating FASTQ quality report";
      break;
    default:
      AR_FAIL("invalid run type");
  }
}

void
print_terminal_postamble(const userconfig& config, bool any_errors)
{
  if (any_errors) {
    switch (config.run_type) {
      case ar_command::trim_adapters:
      case ar_command::demultiplex_only:
        log::error() << "AdapterRemoval did not run to completion;\n"
                     << "    do NOT make use of the resulting reads!";
      case ar_command::benchmark:
      case ar_command::report_only:
        break;
      default:
        AR_FAIL("invalid run type");
    }

    return;
  }

  switch (config.run_type) {
    case ar_command::benchmark:
      log::info() << "Benchmarking complete";
      break;
    case ar_command::trim_adapters:
      log::info() << "Adapter trimming complete";
      break;
    case ar_command::demultiplex_only:
      log::info() << "Demultiplexing complete";
      break;
    case ar_command::report_only:
      log::info() << "FASTQ quality report generation complete";
      break;
    default:
      AR_FAIL("invalid run type");
  }
}

} // namespace adapterremoval

1	/*************************************************************************\
2	* AdapterRemoval - cleaning next-generation sequencing reads *
3	* *
4	* Copyright (C) 2022 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 "commontypes.hpp" // for trimming_strategy, trimming_strategy::mott
20	#include "debug.hpp" // for AR_FAIL
21	#include "logging.hpp" // for info, log_stream, error, warn
22	#include "reports.hpp" // for print_terminal_postamble, print_terminal_...
23	#include "simd.hpp" // for name, instruction_set, instruction_set::none
24	#include "userconfig.hpp" // for userconfig, ar_command, ar_command::demul...
25	#include <string> // for string
26
27	namespace adapterremoval {
28
29	void
30	print_trimming_parameters(const userconfig& config)	×
31	{
32	switch (config.trim) {	×
33	case trimming_strategy::mott:	×
34	log::info() << " - Mott based quality based trimming with max "	×
35	<< "error-rate " << config.trim_mott_rate;	×
36	break;	×
37	case trimming_strategy::window:	×
38	log::info() << " - Window based quality based trimming with window size "	×
39	<< config.trim_window_length << "and minimum quality score "	×
40	<< config.trim_quality_score	×
41	<< (config.trim_ambiguous_bases ? " (including Ns)" : "");	×
42	break;	×
43	case trimming_strategy::per_base:	×
44	if (config.trim_low_quality_bases) {	×
45	log::info() << " - Per-base based quality based trimming with minimum "	×
46	<< "quality score " << config.trim_quality_score	×
47	<< (config.trim_ambiguous_bases ? " (including Ns)" : "");	×
48	} else if (config.trim_ambiguous_bases) {	×
49	log::info() << " - Per-base based trimming of Ns";	×
50	} else {
51	AR_FAIL("this should not be possible");	×
52	}
53	break;
54	case trimming_strategy::none:	×
55	log::info() << " - Quality based trimming disabled";	×
56	break;	×
57
58	default:	×
59	AR_FAIL("not implemented");	×
60	}
61	}
62
63	void
64	print_terminal_preamble(const userconfig& config)	×
65	{
66	log::log_preamble();	×
67
68	if (config.simd == simd::instruction_set::none) {	×
69	log::warn() << "Hardware accelerated alignments disabled!";	×
70	} else {
71	log::info() << "Using " << simd::name(config.simd)	×
72	<< " accelerated alignments";	×
73	}
74
75	switch (config.run_type) {	×
76	case ar_command::trim_adapters:	×
77	if (config.paired_ended_mode) {	×
78	log::info() << "Trimming adapters from PE reads:";	×
79	} else {
80	log::info() << "Trimming adapters from SE reads:";	×
81	}
82
83	print_trimming_parameters(config);	×
84	break;	×
85	case ar_command::benchmark:	×
86	log::info() << "Benchmarking sub-systems";	×
87	break;	×
88	case ar_command::demultiplex_only:	×
89	log::info() << "Demultiplexing reads";	×
90	break;	×
91	case ar_command::report_only:	×
92	log::info() << "Generating FASTQ quality report";	×
93	break;	×
94	default:	×
95	AR_FAIL("invalid run type");	×
96	}
97	}
98
99	void
100	print_terminal_postamble(const userconfig& config, bool any_errors)	×
101	{
102	if (any_errors) {	×
103	switch (config.run_type) {	×
104	case ar_command::trim_adapters:	×
105	case ar_command::demultiplex_only:	×
106	log::error() << "AdapterRemoval did not run to completion;\n"	×
107	<< " do NOT make use of the resulting reads!";	×
108	case ar_command::benchmark:	×
109	case ar_command::report_only:	×
110	break;	×
111	default:	×
112	AR_FAIL("invalid run type");	×
113	}
114
115	return;	×
116	}
117
118	switch (config.run_type) {	×
119	case ar_command::benchmark:	×
120	log::info() << "Benchmarking complete";	×
121	break;	×
122	case ar_command::trim_adapters:	×
123	log::info() << "Adapter trimming complete";	×
124	break;	×
125	case ar_command::demultiplex_only:	×
126	log::info() << "Demultiplexing complete";	×
127	break;	×
128	case ar_command::report_only:	×
129	log::info() << "FASTQ quality report generation complete";	×
130	break;	×
131	default:	×
132	AR_FAIL("invalid run type");	×
133	}
134	}
135
136	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #45

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