MikkelSchubert / adapterremoval / #75

Committed 24 Mar 2025 09:26PM UTC coverage: 27.778% (+0.7%) from 27.088%

Build # #75

Build Type

push

travis-ci

Committed by

web-flow

Commit Message

rework debug serialization (#97)

- Patch catch2 to disable the built-in stringification of objects with
  begin()/end() functions, to prevent complex objects from being mangled
- Specify custom fallbackStringifier function, that uses a StringStream.
  This ensures that support for stringification is present when tests are
  written, rather than objects being emitted as "{?}"
- Replace existing StringMaker implementations with operator<< functions
- Add tests for these functions

Run Details

91 of 103 new or added lines in 8 files covered. (88.35%)

11 existing lines in 3 files now uncovered.

2687 of 9673 relevant lines covered (27.78%)

4228.2 hits per line

Source File
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90.48

/src/sequence.cpp

// SPDX-License-Identifier: GPL-3.0-or-later
// SPDX-FileCopyrightText: 2024 Mikkel Schubert <mikkelsch@gmail.com>
#include "sequence.hpp"  // declarations
#include "fastq_enc.hpp" // for FASTQ_ENCODING_33
#include "strutils.hpp"  // for log_escape
#include <array>         // for array

namespace adapterremoval {

dna_sequence::dna_sequence(std::string seq)
  : m_sequence(std::move(seq))
{
  FASTQ_ENCODING_SAM.process_nucleotides(m_sequence);
}

dna_sequence
dna_sequence::operator+(const dna_sequence& other) const
{
  dna_sequence result;
  result.m_sequence.reserve(length() + other.length());
  result.m_sequence += m_sequence;
  result.m_sequence += other.m_sequence;

  return result;
}

dna_sequence
dna_sequence::reverse_complement() const
{
  // Lookup table for complementary bases based only on the last 4 bits
  static constexpr std::array<char, 16> complements{ '-', 'T', '-', 'G',
                                                     'A', '-', '-', 'C',
                                                     '-', '-', '-', '-',
                                                     '-', '-', 'N', '-' };

  dna_sequence rc;
  rc.m_sequence.reserve(length());
  for (auto it = m_sequence.rbegin(); it != m_sequence.rend(); ++it) {
    rc.m_sequence.push_back(complements[*it & 0xf]);
  }

  return rc;
}

std::ostream&
operator<<(std::ostream& os, const dna_sequence& value)
{
  return os << "dna_sequence{" << log_escape(value) << "}";
}

} // namespace adapterremoval

1	// SPDX-License-Identifier: GPL-3.0-or-later
2	// SPDX-FileCopyrightText: 2024 Mikkel Schubert <mikkelsch@gmail.com>
3	#include "sequence.hpp" // declarations
4	#include "fastq_enc.hpp" // for FASTQ_ENCODING_33
5	#include "strutils.hpp" // for log_escape
6	#include <array> // for array
7
8	namespace adapterremoval {
9
10	dna_sequence::dna_sequence(std::string seq)	394✔
11	: m_sequence(std::move(seq))	394✔
12	{
13	FASTQ_ENCODING_SAM.process_nucleotides(m_sequence);	394✔
14	}	394✔
15
16	dna_sequence
17	dna_sequence::operator+(const dna_sequence& other) const	2✔
18	{
19	dna_sequence result;	2✔
20	result.m_sequence.reserve(length() + other.length());	6✔
21	result.m_sequence += m_sequence;	2✔
22	result.m_sequence += other.m_sequence;	2✔
23
24	return result;	2✔
NEW 25	}	×
26
27	dna_sequence
28	dna_sequence::reverse_complement() const	128✔
29	{
30	// Lookup table for complementary bases based only on the last 4 bits
31	static constexpr std::array<char, 16> complements{ '-', 'T', '-', 'G',	128✔
32	'A', '-', '-', 'C',
33	'-', '-', '-', '-',
34	'-', '-', 'N', '-' };
35
36	dna_sequence rc;	128✔
37	rc.m_sequence.reserve(length());	256✔
38	for (auto it = m_sequence.rbegin(); it != m_sequence.rend(); ++it) {	1,512✔
39	rc.m_sequence.push_back(complements[*it & 0xf]);	750✔
40	}
41
42	return rc;	128✔
NEW 43	}	×
44
45	std::ostream&
46	operator<<(std::ostream& os, const dna_sequence& value)	2✔
47	{
48	return os << "dna_sequence{" << log_escape(value) << "}";	8✔
49	}
50
51	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #75

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