--- /srv/rebuilderd/tmp/rebuilderdSo5ZHD/inputs/seqan3-doc_3.4.0~rc.3+ds-4_all.deb +++ /srv/rebuilderd/tmp/rebuilderdSo5ZHD/out/seqan3-doc_3.4.0~rc.3+ds-4_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2025-04-23 13:22:40.000000 debian-binary │ --rw-r--r-- 0 0 0 81156 2025-04-23 13:22:40.000000 control.tar.xz │ --rw-r--r-- 0 0 0 2744012 2025-04-23 13:22:40.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 81308 2025-04-23 13:22:40.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 2713756 2025-04-23 13:22:40.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./control │ │ │ @@ -1,13 +1,13 @@ │ │ │ Package: seqan3-doc │ │ │ Source: seqan3 │ │ │ Version: 3.4.0~rc.3+ds-4 │ │ │ Architecture: all │ │ │ Maintainer: Debian Med Packaging Team │ │ │ -Installed-Size: 55060 │ │ │ +Installed-Size: 53060 │ │ │ Depends: doxygen-awesome-css │ │ │ Suggests: libseqan3-dev │ │ │ Section: doc │ │ │ Priority: optional │ │ │ Multi-Arch: foreign │ │ │ Homepage: https://www.seqan.de/ │ │ │ Description: C++ library for the analysis of biological sequences v3 (documentation) │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -990,14 +990,15 @@ │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000015_000016.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000015_000027.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000015_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000015_000038.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000015_000068.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000015_000072.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000015_000074.html │ │ │ │ +usr/share/doc/libseqan3-dev/html/dir_000015_000083.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000015_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000016_000012.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000016_000017.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000016_000022.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000016_000025.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000016_000030.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000016_000035.html │ │ │ │ @@ -1134,15 +1135,14 @@ │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000066_000025.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000067_000085.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000068_000015.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000068_000016.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000068_000032.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000068_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000068_000082.html │ │ │ │ -usr/share/doc/libseqan3-dev/html/dir_000068_000086.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000068_000088.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000068_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000069_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000071_000025.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000071_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000072_000014.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000072_000016.html │ │ │ │ @@ -1155,15 +1155,14 @@ │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000073_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000074_000016.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000074_000027.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000074_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000074_000038.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000074_000041.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000074_000072.html │ │ │ │ -usr/share/doc/libseqan3-dev/html/dir_000074_000083.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000074_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000075_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000075_000088.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000075_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000077_000025.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000077_000073.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000079_000035.html │ │ │ │ @@ -1184,14 +1183,15 @@ │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000083_000027.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000083_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000083_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000084_000016.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000084_000029.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000084_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000084_000054.html │ │ │ │ +usr/share/doc/libseqan3-dev/html/dir_000084_000062.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000084_000064.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000084_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000086_000016.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000086_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000086_000050.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000086_000082.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000086_000088.html ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -1,21 +1,21 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./usr/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/ │ │ │ -rw-r--r-- 0 root (0) root (0) 6390 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/aa10li_8hpp.html │ │ │ --rw-r--r-- 0 root (0) root (0) 42652 2025-04-23 13:22:40.000000 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11360 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/about_copyright.html │ │ │ -rw-r--r-- 0 root (0) root (0) 10713 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/about_customisation.html │ │ │ @@ -24,60 +24,60 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 6603 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/adaptor__for__view__without__args_8hpp.html │ │ │ -rw-r--r-- 0 root (0) root (0) 13544 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/adaptor__for__view__without__args_8hpp_source.html │ │ │ -rw-r--r-- 0 root (0) root (0) 6554 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/adaptor__from__functor_8hpp.html │ │ │ -rw-r--r-- 0 root (0) root (0) 14325 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/adaptor__from__functor_8hpp_source.html │ │ │ -rw-r--r-- 0 root (0) root (0) 6391 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/add__enum__bitwise__operators_8hpp.html │ │ │ -rw-r--r-- 0 root 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17
│ │ │
18namespace seqan3
│ │ │
19{
│ │ │
│ │ │
79class aa10li : public aminoacid_base<aa10li, 10>
│ │ │
80{
│ │ │
81private:
│ │ │ -
83 using base_t = aminoacid_base<aa10li, 10>;
│ │ │ +
83 using base_t = aminoacid_base<aa10li, 10>;
│ │ │
84
│ │ │
86 friend base_t;
│ │ │
89 friend base_t::base_t;
│ │ │
91
│ │ │
92public:
│ │ │ -
96 constexpr aa10li() noexcept = default;
│ │ │ -
97 constexpr aa10li(aa10li const &) noexcept = default;
│ │ │ -
98 constexpr aa10li(aa10li &&) noexcept = default;
│ │ │ -
99 constexpr aa10li & operator=(aa10li const &) noexcept = default;
│ │ │ -
100 constexpr aa10li & operator=(aa10li &&) noexcept = default;
│ │ │ -
101 ~aa10li() noexcept = default;
│ │ │ +
96 constexpr aa10li() noexcept = default;
│ │ │ +
97 constexpr aa10li(aa10li const &) noexcept = default;
│ │ │ +
98 constexpr aa10li(aa10li &&) noexcept = default;
│ │ │ +
99 constexpr aa10li & operator=(aa10li const &) noexcept = default;
│ │ │ +
100 constexpr aa10li & operator=(aa10li &&) noexcept = default;
│ │ │ +
101 ~aa10li() noexcept = default;
│ │ │
102
│ │ │ -
104 using base_t::base_t;
│ │ │ +
104 using base_t::base_t;
│ │ │
106
│ │ │ -
107private:
│ │ │ -
109 static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'F', 'G', 'H', 'I', 'J', 'K', 'P'};
│ │ │ +
107private:
│ │ │ +
109 static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'F', 'G', 'H', 'I', 'J', 'K', 'P'};
│ │ │
110
│ │ │ -
112 static constexpr rank_type char_to_rank(char_type const chr)
│ │ │ +
112 static constexpr rank_type char_to_rank(char_type const chr)
│ │ │
113 {
│ │ │
114 using index_t = std::make_unsigned_t<char_type>;
│ │ │ -
115 return char_to_rank_table[static_cast<index_t>(chr)];
│ │ │ +
115 return char_to_rank_table[static_cast<index_t>(chr)];
│ │ │
116 }
│ │ │
117
│ │ │
119 static constexpr char_type rank_to_char(rank_type const rank)
│ │ │
120 {
│ │ │
121 return rank_to_char_table[rank];
│ │ │
122 }
│ │ │
123
│ │ │ @@ -236,28 +236,28 @@ │ │ │
189
│ │ │
190// ------------------------------------------------------------------
│ │ │
191// literals
│ │ │
192// ------------------------------------------------------------------
│ │ │
193inline namespace literals
│ │ │
194{
│ │ │
195
│ │ │ -
209constexpr aa10li operator""_aa10li(char const c) noexcept
│ │ │ +
209constexpr aa10li operator""_aa10li(char const c) noexcept
│ │ │
210{
│ │ │ -
211 return aa10li{}.assign_char(c);
│ │ │ +
211 return aa10li{}.assign_char(c);
│ │ │
212}
│ │ │
213
│ │ │ -
225SEQAN3_WORKAROUND_LITERAL aa10li_vector operator""_aa10li(char const * const s, size_t const n)
│ │ │ +
225SEQAN3_WORKAROUND_LITERAL aa10li_vector operator""_aa10li(char const * const s, size_t const n)
│ │ │
226{
│ │ │ -
227 aa10li_vector r;
│ │ │ -
228 r.resize(n);
│ │ │ +
227 aa10li_vector r;
│ │ │ +
228 r.resize(n);
│ │ │
229
│ │ │ -
230 for (size_t i = 0; i < n; ++i)
│ │ │ -
231 r[i].assign_char(s[i]);
│ │ │ +
230 for (size_t i = 0; i < n; ++i)
│ │ │ +
231 r[i].assign_char(s[i]);
│ │ │
232
│ │ │ -
233 return r;
│ │ │ +
233 return r;
│ │ │
234}
│ │ │
236
│ │ │
237} // namespace literals
│ │ │
238
│ │ │
239} // namespace seqan3
│ │ │
concept.hpp
Provides seqan3::aminoacid_alphabet.
│ │ │
aminoacid_base.hpp
Provides seqan3::aminoacid_base.
│ │ │ @@ -266,21 +266,21 @@ │ │ │
seqan3::aa10li::aa10li
constexpr aa10li() noexcept=default
Defaulted.
│ │ │
seqan3::alphabet_base< aa10li, size, char >
│ │ │
seqan3::alphabet_base::assign_char
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
│ │ │
seqan3::alphabet_base::rank_type
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:77
│ │ │
seqan3::alphabet_base::alphabet_size
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:196
│ │ │
seqan3::alphabet_base::char_type
std::conditional_t< std::same_as< char_t, void >, char, char_t > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition alphabet_base.hpp:69
│ │ │
seqan3::aminoacid_base
A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids.
Definition aminoacid_base.hpp:30
│ │ │ -
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
│ │ │ │ │ │
std::array::fill
T fill(T... args)
│ │ │ │ │ │
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
│ │ │
seqan3::to_lower
constexpr char_type to_lower(char_type const c) noexcept
Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.
Definition transform.hpp:74
│ │ │
SEQAN3_WORKAROUND_LITERAL
#define SEQAN3_WORKAROUND_LITERAL
Our char literals returning std::vector should be constexpr if constexpr std::vector is supported.
Definition platform.hpp:294
│ │ │ +
std::vector::resize
T resize(T... args)
│ │ │
transform.hpp
Provides utilities for modifying characters.
│ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │

Table of Contents

│ │ │ │ │ │
│ │ │

SeqAn3 adheres to semantic versioning and provides a stable API within one major release (all of seqan-3.*.*) unless otherwise noted.

│ │ │

There is no ABI stability.

│ │ │

Many of the rules on this page are derived from the abseil library.

│ │ │

│ │ │ API stability

│ │ │ @@ -153,15 +153,15 @@ │ │ │

In the very rare case that we feel a breaking change to the API is unavoidable, we promise to provide the following update path:

    │ │ │
  • A new minor version is introduced that supports the new API.
    • │ │ │
  • The old API is still supported, but might be marked [[deprecated]].
    • │ │ │
  • We provide very extensive documentation on the change or an automated tool that converts your code from using the old API to using the new API.
    • │ │ │
  • The next (or another future) minor version removes the old API.
    • │ │ │
│ │ │
Warning
As a special case of point 2, the entire 3.0.* release is not stable. We will do our best not to break things, but similar to the releases of GCC, we start labelling entities as stable starting from seqan-3.1.0. Please refer to the documentation of the individual entities for their stability status.
│ │ │ -

│ │ │ +

│ │ │ ABI stability

│ │ │

No guarantees of any kind are provided in regard to the in-memory representation of our data structures. We intend for SeqAn to be built from source. The internal layout of our types may change at any point, without notice. In particular, building SeqAn in the presence of different C++ standard library types may change SeqAn types, especially for pre-adopted types in the std module — these will resolve to standard library types as of C++20.

│ │ │

We do promise, however, that SeqAn3 data structures¹ serialised to disk are de-serialisable by later versions of SeqAn3. The reverse is not true, however, and re-serialising a data structure serialised by a previous release might result in a different (updated) on-disk format.

│ │ │

¹ Iff they are API stable.

│ │ │

│ │ │ Platform stability

│ │ │

The main requirement for SeqAn3 is that your operating system provides one of the compilers supported by us. In general, we only support the latest three major compiler versions. We currently support the following compilers on 64-bit operating systems with little-endian CPU architectures:

    │ │ │ @@ -192,15 +192,15 @@ │ │ │ FreeBSD the latest stable release │ │ │ │ │ │

    "Support" in this context does not imply that we package SeqAn for these operating systems (although we do in some cases), it merely states that you should be able to build applications that depend on SeqAn on the given platforms. This implies the availability of a supported compiler in the default package repositories or via easy-to-use third party services.

    │ │ │

    More platforms and compilers will be added during the SeqAn3 lifecycle, but some will be marked as experimentally supported which means support may be dropped again later on.

    │ │ │

    We promise to provide good forward-compatibility with the C++ standard. And we will strive to fix any warnings that are added by newer versions of a supported compiler.

    │ │ │

    ¹ This site provides a good overview of what the current release and its lifecycle is.
    │ │ │ ² We consider CentOS 7 / RedHat Enterprise Linux (RHEL) 7 as being community-supported. That means issues and patches are welcome, but we do not actively test for those operating systems. See this related issue.

    │ │ │ -

    │ │ │ +

    │ │ │ Dependencies

    │ │ │

    We may add additional dependencies in future minor releases of SeqAn or raise the required versions of current dependencies. However, we promise not to add required dependencies that result in new licensing obligations or link-time dependencies.

    │ │ │
│ │ │ │ │ │ │ │ │ │ │ │
│ │ │

Table of Contents

│ │ │ -
│ │ │

This changelog contains a top-level entry for each release with sections on new features, API changes and notable bug-fixes (not all bug-fixes will be listed).

│ │ │

Get to know SeqAn3 with our tutorials.

│ │ │

Please see the release announcement: https://www.seqan.de/announcing-seqan3/

│ │ │

See the porting guide for some help on porting: https://docs.seqan.de/seqan3/main_user/howto_porting.html

│ │ │

See the documentation on API stability to learn about when API changes are allowed.

│ │ │ -

│ │ │ +

│ │ │ 3.4.0

│ │ │ -

│ │ │ +

│ │ │ New features

│ │ │

I/O

│ │ │ │ │ │ -

│ │ │ +

│ │ │ Notable Bug-fixes

│ │ │

Alphabet

│ │ │ │ │ │

Alignment

│ │ │
    │ │ │
  • Fixed an issue that caused incorrect begin and end positions for banded alignments (#3269).
    • │ │ │
│ │ │

I/O

│ │ │ │ │ │ -

│ │ │ +

│ │ │ API changes

│ │ │

Compiler

│ │ │
    │ │ │
  • Supported compiler:
      │ │ │
    • GCC 12, 13, 14
      • │ │ │
    • Clang 17, 18, 19
      • │ │ │
    • IntelOneAPI/IntelLLVM 2024.0
      • │ │ │ @@ -201,17 +201,17 @@ │ │ │

      Dependencies

      │ │ │
        │ │ │
      • We now use Doxygen version 1.9.8 to build our documentation (#3197).
        • │ │ │
      • We bumped the minimal CMake version to 3.20 (#3314).
        • │ │ │
      • Dependencies are now managed via CPM instead of submodules (#3328).
        • │ │ │
      • The build_system directory was renamed to cmake (#3292).
        • │ │ │
      │ │ │ -

      │ │ │ +

      │ │ │ 3.3.0

      │ │ │ -

      │ │ │ +

      │ │ │ New features

      │ │ │

      Alignment

      │ │ │ │ │ │

      Alphabet

      │ │ │ @@ -224,15 +224,15 @@ │ │ │ │ │ │

      Search

      │ │ │ │ │ │ -

      │ │ │ +

      │ │ │ Notable Bug-fixes

      │ │ │

      Alignment

      │ │ │
        │ │ │
      • Resolved an issue resulting in a wrong alignment score (#3098).
        • │ │ │
      │ │ │

      I/O

      │ │ │ │ │ │

      Utility

      │ │ │
        │ │ │
      • Fixed spin delay having no effect on the PowerPC platform (#3129).
        • │ │ │
      │ │ │ -

      │ │ │ +

      │ │ │ API changes

      │ │ │

      Alignment

      │ │ │ │ │ │

      Compiler

      │ │ │
        │ │ │ @@ -258,17 +258,17 @@ │ │ │

        Dependencies

        │ │ │
          │ │ │
        • We require at least CMake 3.16 for our test suite. Note that the minimum requirement for using SeqAn3 is unchanged (#3050).
          • │ │ │
        • We now use Doxygen version 1.9.6 to build our documentation (#3116).
          • │ │ │
        • Updated sdsl-lite to 3.0.3 (#3170, #3174).
          • │ │ │
        • Compatibility with SeqAn2: SeqAn2's namespace was changed from seqan to seqan2. For interoperability, an up-to-date checkout of SeqAn2's main branch is required (#3156).
          • │ │ │
        │ │ │ -

        │ │ │ +

        │ │ │ 3.2.0

        │ │ │ -

        │ │ │ +

        │ │ │ New features

        │ │ │

        Alphabet

        │ │ │ │ │ │

        I/O

        │ │ │ @@ -279,15 +279,15 @@ │ │ │
          │ │ │
        • Improved performance of seqan3::counting_vector::operator+= (#2930).
          • │ │ │
        │ │ │

        Utility

        │ │ │ │ │ │ -

        │ │ │ +

        │ │ │ Notable Bug-fixes

        │ │ │

        Core

        │ │ │
          │ │ │
        • Added missing implementations for AVX512 (#2920 and #2926).
          • │ │ │
        │ │ │

        IO

        │ │ │
          │ │ │ @@ -301,15 +301,15 @@ │ │ │
        │ │ │

        Utility

        │ │ │
          │ │ │
        • seqan3::views::single_pass_input cannot propagate the std::ranges::output_range property because it cannot satisfy the following requirement (#2775): cpp *it++ = value; // must be the same as *it = value; ++it; // but it actually would be the same as ++it; *it = value;
          • │ │ │
        • Fixed signature of seqan3::detail::store_sse4. This might have affected some public API (#2893).
          • │ │ │
        • Relaxed seqan3::views::to_simd requirements to be C++20-compatible (#2849).
          • │ │ │
        │ │ │ -

        │ │ │ +

        │ │ │ API changes

        │ │ │

        GCC 7, 8, and 9 have been removed. All headers in seqan3/std/ except charconv and new have been deprecated, please use the equivalent std includes. The namespace std::cpp20 has been deprecated, please use std::.

        │ │ │

        seqan3::views::to has been changed to seqan3::ranges::to. Since it is not a view anymore, it cannot be properly deprecated. Please keep this in mind if you encounter errors with seqan3::views::to.

        │ │ │

        Compiler

        │ │ │
          │ │ │
        • Dropped support for GCC 7 and 8 (#2891).
          • │ │ │
        • Dropped support for GCC 9 (#2952).
          • │ │ │ @@ -331,43 +331,43 @@ │ │ │

          Dependencies

          │ │ │
            │ │ │
          • We now use Doxygen version 1.9.4 to build our documentation (#2979).
            • │ │ │
          • Removed range-v3 (#2998).
            • │ │ │
          • Updated cereal to 1.3.2 (#3012).
            • │ │ │
          • Updated sdsl-lite to 3.0.1 (#3012).
            • │ │ │
          │ │ │ -

          │ │ │ +

          │ │ │ 3.1.0

          │ │ │ -

          │ │ │ +

          │ │ │ New features

          │ │ │

          Build system

          │ │ │
            │ │ │
          • We now use Doxygen version 1.9.2 to build our documentation (#2765).
            • │ │ │
          │ │ │ -

          │ │ │ +

          │ │ │ Notable Bug-fixes

          │ │ │

          Argument Parser

          │ │ │
            │ │ │
          • Fixed an issue that led to the wrong option type being printed on errors (#2836).
            • │ │ │
          │ │ │

          Search

          │ │ │
            │ │ │
          • Resolved an issue that prevented the FM-Index from being constructed correctly for inputs larger than 4 GiB (#2756).
            • │ │ │
          │ │ │ -

          │ │ │ +

          │ │ │ API changes

          │ │ │

          The files deprecated in 3.0.3 (denoted by [deleted without replacement]) have been removed.

          │ │ │ -

          │ │ │ +

          │ │ │ 3.0.3

          │ │ │

          Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

          │ │ │
            │ │ │
          • Check out our updated SeqAn3 Cookbook. It contains a listing of code examples on how to perform particular tasks using the library.
            • │ │ │
          • SeqAn 3.0.3 is known to compile with GCC 7.5, 8.4, 9.3, 10.3, and 11.1. Future versions (e.g. GCC 11.2 and 12) might work, but were not yet available at the time of this release.
            • │ │ │
          │ │ │ -

          │ │ │ +

          │ │ │ New features

          │ │ │

          Alphabet

          │ │ │
            │ │ │
          • Added seqan3::phred94, a quality type that represents the full Phred Score range (Sanger format) and is used for PacBio Phred scores of HiFi reads (#2290).
            • │ │ │
          │ │ │

          Argument Parser

          │ │ │

Search

│ │ │ │ │ │ -

│ │ │ +

│ │ │ 3.0.2

│ │ │

Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

│ │ │ │ │ │ -

│ │ │ +

│ │ │ New features

│ │ │

Alignment

│ │ │ │ │ │ @@ -761,15 +761,15 @@ │ │ │ │ │ │

Search

│ │ │ │ │ │ -

│ │ │ +

│ │ │ API changes

│ │ │ │ │ │

Alignment

│ │ │

│ │ │ Notable Bug-fixes

│ │ │

Alignment

│ │ │ │ │ │

Argument Parser

│ │ │ @@ -880,18 +880,18 @@ │ │ │
  • seqan3::fm_index and seqan3::bi_fm_index construct the index correctly if a collection with a single text is passed as input (#1892).
    • │ │ │ │ │ │

    Range

    │ │ │ │ │ │ -

    │ │ │ +

    │ │ │ 3.0.1

    │ │ │

    Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

    │ │ │ -

    │ │ │ +

    │ │ │ New features

    │ │ │

    Alphabet

    │ │ │ │ │ │

    Alignment

    │ │ │ @@ -939,15 +939,15 @@ │ │ │ │ │ │

    Std

    │ │ │ │ │ │ -

    │ │ │ +

    │ │ │ API changes

    │ │ │ │ │ │

    Alphabet

    │ │ │ @@ -994,15 +994,15 @@ │ │ │

    Search

    │ │ │ │ │ │ -

    │ │ │ +

    │ │ │ Notable Bug-fixes

    │ │ │