#106

Committed 28 Apr 2025 11:42AM UTC coverage: 66.997% (+0.07%) from 66.927%

Build # #106

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

gather phred<->p code and fix reported mott value (#132)

Run Details

42 of 47 new or added lines in 6 files covered. (89.36%)

8 existing lines in 1 file now uncovered.

9732 of 14526 relevant lines covered (67.0%)

3044.2 hits per line

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0.0

/src/reports_terminal.cpp

// SPDX-License-Identifier: GPL-3.0-or-later
// SPDX-FileCopyrightText: 2022 Mikkel Schubert <mikkelsch@gmail.com>
#include "commontypes.hpp" // for trimming_strategy, trimming_strategy::mott
#include "debug.hpp"       // for AR_FAIL
#include "fastq_enc.hpp"   // for fastq_encoding
#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 <iomanip>         // for fixed, setprecision
#include <string>          // for string

namespace adapterremoval {

void
print_trimming_parameters(const userconfig& config)
{
  switch (config.trim) {
    case trimming_strategy::mott:
      log::info() << "  - Mott based trimming with Phred encoded quality score "
                  << std::fixed << std::setprecision(1)
                  << fastq_encoding::p_to_phred(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	// SPDX-License-Identifier: GPL-3.0-or-later
2	// SPDX-FileCopyrightText: 2022 Mikkel Schubert <mikkelsch@gmail.com>
3	#include "commontypes.hpp" // for trimming_strategy, trimming_strategy::mott
4	#include "debug.hpp" // for AR_FAIL
5	#include "fastq_enc.hpp" // for fastq_encoding
6	#include "logging.hpp" // for info, log_stream, error, warn
7	#include "reports.hpp" // for print_terminal_postamble, print_terminal_...
8	#include "simd.hpp" // for name, instruction_set, instruction_set::none
9	#include "userconfig.hpp" // for userconfig, ar_command, ar_command::demul...
10	#include <iomanip> // for fixed, setprecision
11	#include <string> // for string
12
13	namespace adapterremoval {
14
15	void
16	print_trimming_parameters(const userconfig& config)	×
17	{
18	switch (config.trim) {	×
19	case trimming_strategy::mott:	×
NEW 20	log::info() << " - Mott based trimming with Phred encoded quality score "	×
NEW 21	<< std::fixed << std::setprecision(1)	×
NEW 22	<< fastq_encoding::p_to_phred(config.trim_mott_rate);	×
23	break;	×
24	case trimming_strategy::window:	×
25	log::info() << " - Window based quality based trimming with window size "	×
26	<< config.trim_window_length << "and minimum quality score "	×
27	<< config.trim_quality_score	×
28	<< (config.trim_ambiguous_bases ? " (including Ns)" : "");	×
29	break;	×
30	case trimming_strategy::per_base:	×
31	if (config.trim_low_quality_bases) {	×
32	log::info() << " - Per-base based quality based trimming with minimum "	×
33	<< "quality score " << config.trim_quality_score	×
34	<< (config.trim_ambiguous_bases ? " (including Ns)" : "");	×
35	} else if (config.trim_ambiguous_bases) {	×
36	log::info() << " - Per-base based trimming of Ns";	×
37	} else {
38	AR_FAIL("this should not be possible");	×
39	}
40	break;
41	case trimming_strategy::none:	×
42	log::info() << " - Quality based trimming disabled";	×
43	break;	×
44
45	default:	×
46	AR_FAIL("not implemented");	×
47	}
48	}
49
50	void
51	print_terminal_preamble(const userconfig& config)	×
52	{
53	log::log_preamble();	×
54
55	if (config.simd == simd::instruction_set::none) {	×
56	log::warn() << "Hardware accelerated alignments disabled!";	×
57	} else {
58	log::info() << "Using " << simd::name(config.simd)	×
59	<< " accelerated alignments";	×
60	}
61
62	switch (config.run_type) {	×
63	case ar_command::trim_adapters:	×
64	if (config.paired_ended_mode) {	×
65	log::info() << "Trimming adapters from PE reads:";	×
66	} else {
67	log::info() << "Trimming adapters from SE reads:";	×
68	}
69
70	print_trimming_parameters(config);	×
71	break;	×
72	case ar_command::benchmark:	×
73	log::info() << "Benchmarking sub-systems";	×
74	break;	×
75	case ar_command::demultiplex_only:	×
76	log::info() << "Demultiplexing reads";	×
77	break;	×
78	case ar_command::report_only:	×
79	log::info() << "Generating FASTQ quality report";	×
80	break;	×
81	default:	×
82	AR_FAIL("invalid run type");	×
83	}
84	}
85
86	void
87	print_terminal_postamble(const userconfig& config, bool any_errors)	×
88	{
89	if (any_errors) {	×
90	switch (config.run_type) {	×
91	case ar_command::trim_adapters:	×
92	case ar_command::demultiplex_only:	×
93	log::error() << "AdapterRemoval did not run to completion;\n"	×
94	<< " do NOT make use of the resulting reads!";	×
95	case ar_command::benchmark:	×
96	case ar_command::report_only:	×
97	break;	×
98	default:	×
99	AR_FAIL("invalid run type");	×
100	}
101
102	return;	×
103	}
104
105	switch (config.run_type) {	×
106	case ar_command::benchmark:	×
107	log::info() << "Benchmarking complete";	×
108	break;	×
109	case ar_command::trim_adapters:	×
110	log::info() << "Adapter trimming complete";	×
111	break;	×
112	case ar_command::demultiplex_only:	×
113	log::info() << "Demultiplexing complete";	×
114	break;	×
115	case ar_command::report_only:	×
116	log::info() << "FASTQ quality report generation complete";	×
117	break;	×
118	default:	×
119	AR_FAIL("invalid run type");	×
120	}
121	}
122
123	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #106

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