SeqAn 3.2.0

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.

🎉 New Features

We added GCC 12 support!

Alphabet

• seqan3::cigar can now be assigned from std::string_view which is much faster (no allocations) than the former assignment from seqan3::small_string.
• The new view seqan3::views::char_strictly_to behaves like seqan3::views::char_to, but throws on invalid input.

I/O

• The new option seqan3::sequence_file_option::fasta_ignore_blanks_before_id lets 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_id will only store "some_id" as ID.
  E.g., fasta_ignore_blanks_before_id = false: >    some_id will store "    some_id" as ID.

Search

• Improved performance of seqan3::counting_vector::operator+= by 25%.

Utility

• Added seqan3::list_traits::repeat.

🛠️ Notable API changes

seqan3::views::to is no view anymore but C++23 conform

We replaced 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 seqan3::views::to.

Example:

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 seqan3/std/ except charconv and new have been deprecated, since their STL-equivalents are available in GCC >= 10. Please use the equivalent std includes.

Example:

// Before
#include <seqan3/std/bit>
#include <seqan3/std/charconv>
// After
#include <bit>
#include <seqan3/std/charconv>

Removed namespace std::cpp20

The namespace 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:: namespace.

Example:

std::ranges::copy(range, std::cpp20::back_inserter(other_range)); // Before
std::ranges::copy(range, std::back_inserter(other_range)); // After

🐛 Notable bug fixes

Core

• Added missing implementations for AVX512 .

IO

• FASTA files containing IDs starting with >, e.g., > >MyID, are now parsed correctly.

Search

• Relaxed kmer_hash_view::iterator difference requirement .
• Relaxed seqan3::views::minimiser requirements to be C++20-compatible.
• Relaxed seqan3::views::kmer_hash requirements to be C++20-compatible.

Utility

• seqan3::views::single_pass_input cannot propagate the std::ranges::output_range property 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.
• Relaxed seqan3::views::to_simd requirements to be C++20-compatible.

🔌 External dependencies

• 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.