[Seqan-dev] SeqAn Release 3.0.1

["Seiler, Enrico Frank" <enrico.seiler@fu-berlin.de>]

We are excited to present a new update of our SeqAn library. This release has been in the making for roughly half a year now and we are proud to present some great new features and also a lot of improvements with respect to runtime and usability. You can 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.

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