SeqAn3  3.2.0-rc.1
The Modern C++ library for sequence analysis.
phred_base.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2022, Knut Reinert & MPI für molekulare Genetik
4 // This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5 // shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
6 // -----------------------------------------------------------------------------------------------------
7 
13 #pragma once
14 
16 #include <seqan3/alphabet/detail/convert.hpp>
18 
19 namespace seqan3
20 {
21 
29 template <typename derived_type, size_t size>
30 class phred_base : public alphabet_base<derived_type, size, char>
31 {
32 public:
40  using phred_type = int8_t;
42 
43 private:
46 
48  friend base_t;
49 
53  constexpr phred_base() noexcept = default;
54  constexpr phred_base(phred_base const &) noexcept = default;
55  constexpr phred_base(phred_base &&) noexcept = default;
56  constexpr phred_base & operator=(phred_base const &) noexcept = default;
57  constexpr phred_base & operator=(phred_base &&) noexcept = default;
58  ~phred_base() noexcept = default;
59 
61  friend derived_type;
62 
63 public:
64  // Import from base type:
65  using base_t::alphabet_size;
66  using base_t::assign_rank;
67  using base_t::to_rank;
68  using typename base_t::char_type;
69  using typename base_t::rank_type;
70 
74  // This constructor needs to be public, because constructor templates are not inherited otherwise
79  template <typename other_qual_type>
80  requires (!std::same_as<phred_base, other_qual_type>)
81  && (!std::same_as<derived_type, other_qual_type>) && quality_alphabet<other_qual_type>
82  explicit constexpr phred_base(other_qual_type const & other) noexcept
83  {
84  assign_phred_to(seqan3::to_phred(other), static_cast<derived_type &>(*this));
85  }
87 
97  constexpr phred_type to_phred() const noexcept
98  {
99  return rank_to_phred[to_rank()];
100  }
102 
122  constexpr derived_type & assign_phred(phred_type const p) noexcept
123  {
124  return assign_rank(phred_to_rank[static_cast<rank_type>(p)]);
125  }
127 
128 private:
130  static constexpr std::array<rank_type, 256> phred_to_rank{[]() constexpr {std::array<rank_type, 256> ret{};
131 
132  for (int64_t i = std::numeric_limits<phred_type>::lowest(); i <= std::numeric_limits<phred_type>::max(); ++i)
133  {
134  if (i < derived_type::offset_phred) // map too-small to smallest possible
135  ret[static_cast<rank_type>(i)] = 0;
136  else if (i >= derived_type::offset_phred + alphabet_size) // map too-large to highest possible
137  ret[static_cast<rank_type>(i)] = alphabet_size - 1;
138  else // map valid range to identity
139  ret[static_cast<rank_type>(i)] = i - derived_type::offset_phred;
140  }
141  return ret;
142 }()
143 }; // namespace seqan3
144 
147  []() constexpr {std::array<phred_type, alphabet_size> ret{};
148 
149 for (size_t i = 0; i < alphabet_size; ++i)
150  ret[i] = i + derived_type::offset_phred;
151 
152 return ret;
153 }
154 ()
155 }
156 ;
157 
159 static constexpr rank_type char_to_rank(char_type const chr)
160 {
161  int64_t difference = static_cast<int64_t>(chr) - static_cast<int64_t>(derived_type::offset_char);
162  return std::clamp<int64_t>(difference, 0, alphabet_size - 1);
163 }
164 
166 static constexpr char_type rank_to_char(rank_type const rank)
167 {
168  return rank + derived_type::offset_char;
169 }
170 }
171 ;
172 
173 } // namespace seqan3
Quality alphabet concept.
Provides seqan3::alphabet_base.
A CRTP-base that makes defining a custom alphabet easier.
Definition: alphabet_base.hpp:57
constexpr rank_type to_rank() const noexcept
Return the letter's numeric value (rank in the alphabet).
Definition: alphabet_base.hpp:137
detail::min_viable_uint_t< size - 1 > rank_type
The type of the alphabet when represented as a number (e.g. via to_rank()).
Definition: alphabet_base.hpp:80
static constexpr detail::min_viable_uint_t< size > alphabet_size
The size of the alphabet, i.e. the number of different values it can take.
Definition: alphabet_base.hpp:199
constexpr derived_type & assign_rank(rank_type const c) noexcept
Assign from a numeric value.
Definition: alphabet_base.hpp:187
std::conditional_t< std::same_as< char, void >, char, char > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition: alphabet_base.hpp:72
A CRTP-base that refines seqan3::alphabet_base and is used by the quality alphabets.
Definition: phred_base.hpp:31
static constexpr std::array< phred_type, alphabet_size > rank_to_phred
Assign from the numeric Phred score value.
Definition: phred_base.hpp:145
static constexpr char_type rank_to_char(rank_type const rank)
Definition: phred_base.hpp:165
static constexpr rank_type char_to_rank(char_type const chr)
Definition: phred_base.hpp:158
int8_t phred_type
The integer representation of the quality score.
Definition: phred_base.hpp:40
constexpr auto to_phred
The public getter function for the Phred representation of a quality score.
Definition: alphabet/quality/concept.hpp:100
constexpr auto assign_phred_to
Assign a Phred score to a quality alphabet object.
Definition: alphabet/quality/concept.hpp:230
requires requires
The rank_type of the semi-alphabet; defined as the return type of seqan3::to_rank....
Definition: alphabet/concept.hpp:164
A concept that indicates whether an alphabet represents quality scores.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.