Re: [Seqan-dev] SeqAn Release 3.0.1

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

Thanks very much

- I hope the problems will be solved soon
- some bugs
--  .. the semaphore.h file missed
--      when running on Windows and Code::Blocks
       or
       on Cygwin


On 1/23/20, Rahn, René <Rene.Rahn@fu-berlin.de> wrote:
> Dear Diaa Fayed,
>
> thank you very much for writing us. We appreciate your feedback.
> Can I ask you if there are features you are missing in particular?
>
> The goal of SeqAn3 is to reduce the code complexity with the help of modern
> C++, while still providing cutting edge algorithms and data structures for
> the bioinformatics community.
> The implied changes to an existing program might be overwhelming at first
> but we believe there is a long-term benefit from that.
> Some of these benefits include that errors are easier to track, coding can
> be much faster through easier interfaces and less boiler plate code and our
> design goes well with new features from the standard library to get the most
> out of your tools.
> The other reason is that SeqAn2 has reached its end-of-life. There will
> likely be a last bug-fix release that improves compatibility with SeqAn3,
> but I am afraid that no further resources can be invested into keeping it up
> to date or fixing newly-found issues.
>
> Regarding the advanced C++ concepts that are fairly new: We are going to
> provide more and more teaching materials as well as try to be around on
> conferences to teach those concepts and introduce features of the library.
> We will inform you via our channels of any of those opportunities.
>
> Of course, we have to admit that at the moment not all interfaces or
> features are complete and that it might be that some interfaces might change
> until 3.1 is fixed.
> On the other hand we'd like to hear from the community what their experience
> with the new library is so we can learn from them, improve the interfaces
> and provide a better high-quality and sustainable software for the
> community.
>
> So if you are critical of these changes, we would be particularly interested
> in your feedback if you do have the chance to try out SeqAn3!
>
> Yours sincerely,
>
> The SeqAn Team
>
>> On 22. Jan 2020, at 19:10, Diaa Fayed <dr.diaafayed@gmail.com> wrote:
>>
>> - 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?
>> ------------------------------------------------------------------------------------------------
>>
>> 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
>>>
>>>
>>
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