Dear SeqAn users, supporters, and subscribers,
we are excited to announce the SeqAn 3.2.0 release that has a major compiler update:
We dropped GCC 7, GCC 8, and GCC 9 and we added GCC 12 support.
As a consequence, we also dropped C++17 support and are fully C++20 compatible.
Furthermore, we could drop the range-v3 dependency completely, so be sure to delete the submodule after updating to SeqAn 3.2.0!
While we will present essential changes of the 3.2.0 release in this message, you can also find a comprehensive list of the changes in our changelog.
Get to know SeqAn3 with our tutorials.
- Visit our API documentation.
- See the porting guide for some help on porting from SeqAn2.
- Check out our SeqAn3 Cookbook. It contains a listing of code examples on how to perform particular tasks using the library.
We added GCC 12 support!
seqan3::cigarcan now be assigned from
std::string_viewwhich is much faster (no allocations) than the former assignment from
- The new view
seqan3::views::char_to, but throws on invalid input.
- The new option
seqan3::sequence_file_option::fasta_ignore_blanks_before_idlets you keep blanks before IDs when reading FASTA files. This ensures a “perfekt roundtrip” when reading and writing FASTA files. E.g., fasta_ignore_blanks_before_id = true (default):
> some_idwill only store
"some_id"as ID. E.g., fasta_ignore_blanks_before_id = false:
> some_idwill store
" some_id"as ID.
- Improved performance of
Notable API changes
seqan3::views::to is no view anymore but C++23 conform
seqan3::views::to (implemented via range-v3) with
seqan3::ranges::to (implemented in SeqAn3).
seqan3::ranges::to provides a subset of C++23’s
std::ranges::to and will be replaced with the STL-equivalent in a future version.
Since it is not a view anymore, it cannot be properly deprecated. Please keep this in mind if you encounter errors with
auto vec = std::views::iota(0, 10) | seqan3::views::to<std::vector>; // Before auto vec = std::views::iota(0, 10) | seqan3::ranges::to<std::vector>(); // After
Removed several headers in seqan3/std/
All headers in
new have been deprecated, since their STL-equivalents are available in GCC >= 10. Please use the equivalent
// Before #include <seqan3/std/bit> #include <seqan3/std/charconv> // After #include <bit> #include <seqan3/std/charconv>
Removed namespace std::cpp20
std::cpp20 has been deprecated, since, e.g., the implementation of the
std::back_inserter among others are now C++20-conform with GCC >= 10. Please use the
std::ranges::copy(range, std::cpp20::back_inserter(other_range)); // Before std::ranges::copy(range, std::back_inserter(other_range)); // After
Notable bug fixes
- Added missing implementations for AVX512 .
- FASTA files containing IDs starting with
> >MyID, are now parsed correctly.
kmer_hash_view::iteratordifference requirement .
seqan3::views::minimiserrequirements to be C++20-compatible.
seqan3::views::kmer_hashrequirements to be C++20-compatible.
seqan3::views::single_pass_inputcannot propagate the
std::ranges::output_rangeproperty because it cannot satisfy the following requirement:
*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.
seqan3::views::to_simdrequirements to be C++20-compatible.
- GCC 7, 8, and 9 have been removed.
- SeqAn 3.2.0 is known to compile with GCC 10.3, 11.3, and 12.1. Future versions might work, but were not yet available at the time of this release.
- Other compilers, e.g., clang, and MSVC, are known to not be compatible with SeqAn 3.2.0.
- We removed range-v3, and now require cereal 1.3.2 as well as sdsl-lite 3.0.1.
- We use doxygen 1.9.4 to build our documentation.