MikkelSchubert / adapterremoval / #46

Committed 27 Nov 2024 03:10PM UTC coverage: 27.245% (+1.0%) from 26.244%

Build # #46

Build Type

push

travis-ci

Committed by

MikkelSchubert

Commit Message

fix convenience executable make target

Run Details

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44.44

/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 barcode_match;
struct next_subsequence;

/** The sample/barcode IDs associated with a set of sequences */
struct barcode_key
{
  constexpr static const int32_t unidentified = -1;
  constexpr static const int32_t ambiguous = -2;

  //! Sample identified by 1 or more barcodes
  int32_t sample = unidentified;
  //! The specific barcode(s) used to identify this sample
  int32_t barcode = unidentified;

  bool operator==(const barcode_key& other) const
  {
    return sample == other.sample && barcode == other.barcode;
  }

  bool operator<(const barcode_key& other) const
  {
    return sample < other.sample ||
           (sample == other.sample && barcode < other.barcode);
  }
};

using barcode_pair = std::pair<sequence_pair, barcode_key>;
using barcode_vec = std::vector<barcode_pair>;

/**
 * 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 barcode_node
{
  barcode_node();

  std::array<int32_t, 4> children;
  barcode_key key;
};

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

  [[nodiscard]] barcode_key identify(const fastq& read_r1) const;
  [[nodiscard]] barcode_key identify(const fastq& read_r1,
                                     const fastq& read_r2) const;

  /** Returns the length of barcodes in read 1  */
  [[nodiscard]] size_t length_1() const { return m_barcode_1_len; }

  /** Returns the length of barcodes in read 2  */
  [[nodiscard]] size_t length_2() const { return m_barcode_2_len; }

private:
  barcode_match lookup(const char* seq,
                       int32_t parent,
                       size_t max_global_mismatches,
                       const char* next) const;

  barcode_match lookup_with_mm(const char* seq,
                               int32_t parent,
                               size_t max_global_mismatches,
                               size_t max_local_mismatches,
                               const char* next) const;

  std::vector<barcode_node> 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 barcode_match;
33	struct next_subsequence;
34
35	/** The sample/barcode IDs associated with a set of sequences */
36	struct barcode_key	465✔
37	{
38	constexpr static const int32_t unidentified = -1;
39	constexpr static const int32_t ambiguous = -2;
40
41	//! Sample identified by 1 or more barcodes
42	int32_t sample = unidentified;
43	//! The specific barcode(s) used to identify this sample
44	int32_t barcode = unidentified;
45
46	bool operator==(const barcode_key& other) const	161✔
47	{
48	return sample == other.sample && barcode == other.barcode;	161✔
49	}
50
51	bool operator<(const barcode_key& other) const	×
52	{
53	return sample < other.sample \|\|	×
54	(sample == other.sample && barcode < other.barcode);	×
55	}
56	};
57
58	using barcode_pair = std::pair<sequence_pair, barcode_key>;
59	using barcode_vec = std::vector<barcode_pair>;
60
61	/**
62	* Struct representing node in quad-tree; children are referenced using the
63	* corresponding index in the vector representing the tree; -1 is used to
64	* represent unassigned children.
65	*/
66	struct barcode_node
67	{
68	barcode_node();
69
70	std::array<int32_t, 4> children;
71	barcode_key key;
72	};
73
74	/**
75	*
76	*/
77	class barcode_table	62✔
78	{
79	public:
80	barcode_table(const sample_set& samples,
81	size_t max_mm,
82	size_t max_mm_r1,
83	size_t max_mm_r2);
84
85	[[nodiscard]] barcode_key identify(const fastq& read_r1) const;
86	[[nodiscard]] barcode_key identify(const fastq& read_r1,
87	const fastq& read_r2) const;
88
89	/** Returns the length of barcodes in read 1 */
90	[[nodiscard]] size_t length_1() const { return m_barcode_1_len; }	×
91
92	/** Returns the length of barcodes in read 2 */
93	[[nodiscard]] size_t length_2() const { return m_barcode_2_len; }	×
94
95	private:
96	barcode_match lookup(const char* seq,
97	int32_t parent,
98	size_t max_global_mismatches,
99	const char* next) const;
100
101	barcode_match lookup_with_mm(const char* seq,
102	int32_t parent,
103	size_t max_global_mismatches,
104	size_t max_local_mismatches,
105	const char* next) const;
106
107	std::vector<barcode_node> m_nodes{};
108	size_t m_max_mismatches = 0;
109	size_t m_max_mismatches_r1 = 0;
110	size_t m_max_mismatches_r2 = 0;
111	size_t m_barcode_1_len = 0;
112	size_t m_barcode_2_len = 0;
113	};
114
115	} // namespace adapterremoval

MikkelSchubert / adapterremoval / #46

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