Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.
Notable new features
-
We added support for type erasing
semialphabets that
allows you to manage semialphabets with the same alphabet size in one container. This can have a big effect on your compile-time, in case you don't drink as much
as
we do.
-
We added parallel support for the alignment algorithm. You can now configure the number of threads you want to use for the alignment computation.
-
One to command them all: Our argument parser now supports
subcommands, such as
git
pull
. A
How-to will guide you through setting this up for your tool.
-
The performance of the I/O was improved to allow faster file reading. Further, we added
support for reading and writing the CIGAR string through alignment files.
-
We added several new ranges and views. Most notably, the seqan3::views::kmer_hash
view, which
transforms a sequence into a range of k-mer hashes efficiently. Another view of great practice is the seqan3::views::to
, which can be used to convert a view into a container. We also added aseqan3::dynamic_bitset
which
is a dynamic version of the std::bitset
.
-
Memory consumption of the (bidirectional) FM-Index for text collections was reduced by 10%.
Notable API changes
As much as we'd like to reduce inconsistencies between releases, we are sometimes forced to change an interface either to improve usability or to follow changes made by the ISO C++ committee.
- All our concepts are named in the
snake_case
style (e.g. seqan3::WritableAlphabet
-> seqan3::writable_alphabet
)! - The directory
seqan3/range/view
has been renamed to seqan3/range/views
. - The namespace
seqan3::view
has been renamed to seqan3::views
. - The CMake variable
SEQAN3_VERSION_STRING
defined by find_package(SEQAN3)
was
renamed to SEQAN3_VERSION
.
You can find a comprehensive list of the changes in our
changelog.
Notable bug fixes
- Copying and moving the
seqan3::fm_index
and seqan3::bi_fm_index
now
work properly. - The translation table for nucleotide to amino acid translation was corrected.
- The amino acid score matrices were corrected.
External dependencies
- We now support ranges-v3 versions >= 0.10.0 and < 0.11.0, increasing the previous requirement of >= 0.5.0 and < 0.6.0.
- We now support cereal version 1.3.0, increasing the previous requirement of 1.2.2