Re: [Seqan-dev] SeqAn Release 3.0.1

[Diaa Fayed <dr.diaafayed@gmail.com>]

- I read about both SeqAn3 and SeqAn2.
- Documentation and some algorithms have not implemented yet in SeqAn3
- SeqAn3 is based on very advanced C++ concepts I have not known about  yet

so

I prefer to use SeqAn2.4

what is your opinion?
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On 1/22/20, Seiler, Enrico Frank <enrico.seiler@fu-berlin.de> wrote:
> 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<http://docs.seqan.de/seqan/3.0.1/about_changelog.html#autotoc_md198>.
>
>   *   Get to know SeqAn3 with our
> tutorials<http://docs.seqan.de/seqan/3-master-user/usergroup1.html>.
>   *   Visit our API
> documentation<http://docs.seqan.de/seqan/3.0.1/index.html>.
>   *   See the porting
> guide<http://docs.seqan.de/seqan/3-master-user/howto_porting.html> 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.
> [tada] Notable new features
>
>   *
> We added support for type erasing
> semialphabets<http://docs.seqan.de/seqan/3.0.1/interfaceseqan3_1_1semialphabet.html>
> 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 [coffee]  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<https://docs.seqan.de/seqan/3.0.1/subcommand_arg_parse.html> 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%.
>
> [:trollface:] 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<http://docs.seqan.de/seqan/3.0.1/about_changelog.html#autotoc_md198>.
> [bug] 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.
>
> [electric_plug] 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
>
>