MikkelSchubert / adapterremoval / #45

Committed 20 Sep 2024 06:49PM UTC coverage: 26.244% (-49.2%) from 75.443%

Build # #45

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push

travis-ci

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web-flow

Commit Message

attempt to fix coveralls run

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2458 of 9366 relevant lines covered (26.24%)

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33.33

/src/barcode_table.hpp

/*************************************************************************\
 * 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/>. *
\*************************************************************************/
#pragma once

#include "sequence.hpp" // for sequence_pair_vec
#include <array>        // for array
#include <cstddef>      // for size_t
#include <cstdint>      // for int32_t
#include <vector>       // for vector

namespace adapterremoval {

class sample_set;
class fastq;
struct next_subsequence;

/**
 * Struct representing node in quad-tree; children are referenced using the
 * corresponding index in the vector representing the tree; -1 is used to
 * represent unassigned children.
 */
struct demultiplexer_node
{
  demultiplexer_node();

  std::array<int32_t, 4> children;
  int value;
};

using demux_node_vec = std::vector<demultiplexer_node>;

/**
 *
 */
class barcode_table
{
public:
  barcode_table(const sample_set& samples,
                size_t max_mm,
                size_t max_mm_r1,
                size_t max_mm_r2);

  barcode_table(const sequence_pair_vec& barcodes,
                size_t max_mm,
                size_t max_mm_r1,
                size_t max_mm_r2);

  int identify(const fastq& read_r1) const;
  int identify(const fastq& read_r1, const fastq& read_r2) const;

  [[nodiscard]] size_t length_1() const { return m_barcode_1_len; }

  [[nodiscard]] size_t length_2() const { return m_barcode_2_len; }

  constexpr static const int no_match = -1;
  constexpr static const int ambiguous = -2;

private:
  struct candidate
  {
    explicit candidate(int barcode = barcode_table::no_match,
                       size_t mismatches = -1);

    int barcode;
    size_t mismatches;
  };

  candidate lookup(const char* seq,
                   int parent,
                   size_t max_global_mismatches,
                   const next_subsequence* next) const;

  candidate lookup_with_mm(const char* seq,
                           int parent,
                           size_t max_global_mismatches,
                           size_t max_local_mismatches,
                           const next_subsequence* next) const;

  demux_node_vec m_nodes{};
  size_t m_max_mismatches = 0;
  size_t m_max_mismatches_r1 = 0;
  size_t m_max_mismatches_r2 = 0;
  size_t m_barcode_1_len = 0;
  size_t m_barcode_2_len = 0;
};

} // namespace adapterremoval

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	#pragma once
21
22	#include "sequence.hpp" // for sequence_pair_vec
23	#include <array> // for array
24	#include <cstddef> // for size_t
25	#include <cstdint> // for int32_t
26	#include <vector> // for vector
27
28	namespace adapterremoval {
29
30	class sample_set;
31	class fastq;
32	struct next_subsequence;
33
34	/**
35	* Struct representing node in quad-tree; children are referenced using the
36	* corresponding index in the vector representing the tree; -1 is used to
37	* represent unassigned children.
38	*/
39	struct demultiplexer_node
40	{
41	demultiplexer_node();
42
43	std::array<int32_t, 4> children;
44	int value;
45	};
46
47	using demux_node_vec = std::vector<demultiplexer_node>;
48
49	/**
50	*
51	*/
52	class barcode_table	64✔
53	{
54	public:
55	barcode_table(const sample_set& samples,
56	size_t max_mm,
57	size_t max_mm_r1,
58	size_t max_mm_r2);
59
60	barcode_table(const sequence_pair_vec& barcodes,
61	size_t max_mm,
62	size_t max_mm_r1,
63	size_t max_mm_r2);
64
65	int identify(const fastq& read_r1) const;
66	int identify(const fastq& read_r1, const fastq& read_r2) const;
67
68	[[nodiscard]] size_t length_1() const { return m_barcode_1_len; }	×
69
70	[[nodiscard]] size_t length_2() const { return m_barcode_2_len; }	×
71
72	constexpr static const int no_match = -1;
73	constexpr static const int ambiguous = -2;
74
75	private:
76	struct candidate
77	{
78	explicit candidate(int barcode = barcode_table::no_match,
79	size_t mismatches = -1);
80
81	int barcode;
82	size_t mismatches;
83	};
84
85	candidate lookup(const char* seq,
86	int parent,
87	size_t max_global_mismatches,
88	const next_subsequence* next) const;
89
90	candidate lookup_with_mm(const char* seq,
91	int parent,
92	size_t max_global_mismatches,
93	size_t max_local_mismatches,
94	const next_subsequence* next) const;
95
96	demux_node_vec m_nodes{};
97	size_t m_max_mismatches = 0;
98	size_t m_max_mismatches_r1 = 0;
99	size_t m_max_mismatches_r2 = 0;
100	size_t m_barcode_1_len = 0;
101	size_t m_barcode_2_len = 0;
102	};
103
104	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #45

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