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    Enrico Seiler
    @eseiler

    Hi, I have a question about shapes, why is it helpful to have a shape with no gap in the start and end position? Like: 100111001

    00010011100100 would be the same as 100111001, gaps at begin/end do not really help since you can just omit them.

    Ahmad lutfi
    @ah_ol_twitter
    Ok thanks
    Lydia Buntrock
    @Irallia
    Since Knut has just sent the new regulations for work, I wanted to offer that I'm open to share my office if that helps someone. :) Jongkyu doesn't seem to show up anymore and so I have the room for myself. If things get tight, I can stay at home for some days and offer you my room.
    Michael R. Crusoe
    @mr-c
    Huh, Tübingen has told me that they won't count any of my work experience before I obtained my degree. I was a nontraditional student and I worked in professional positions for over 10 years prior to receiving my B.S. in microbiology :-(
    Hannes Hauswedell
    @h-2
    It's not untypical. FU didn't count my time when I received a stipend as prior experience, and I was literally doing THE SAME THING during stipend time that I did later on the job :(
    If you are not member of a trade union, I would suggest joining GEW and have them check the whole thing. Could make a big difference.
    Michael R. Crusoe
    @mr-c
    @h-2 thanks for the tip!
    simonsasse
    @simonsasse
    Hi, how do seqan2 and seqan3 treat the unknown characters in Dna5 and Rna5 when aligning ? :)
    Enrico Seiler
    @eseiler
    The default is mismatch(hamming distance, N only matches with N). In general, it depends on the scoring scheme you are using - it is treating them the way you want them to be treated.
    simonsasse
    @simonsasse
    thanks a lot for the fast answer !
    Michael R. Crusoe
    @mr-c
    Is it time for a new SeqAn release? We've got another GCC 10 bug in Debian which could result in the package being removed: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=966270
    3 replies
    GCC version: 10.1.0
    Michael R. Crusoe
    @mr-c

    With gcc 10.2.0 and `-std=c++17 -fconcepts' (which just entered Debian)

    /build/seqan3-3.0.1+ds/include/seqan3/alphabet/concept.hpp:759:39: error: comparison is always true due to limited range of data type [-Werror=type-limits]

    Internal compiler error: Error reporting routines re-entered.

    Michael R. Crusoe
    @mr-c
    seqan/seqan3#1993 has the details
    Michael R. Crusoe
    @mr-c
    @marehr hmm.. gcc 10.2 is still not happy https://github.com/seqan/seqan3/issues/1993#issuecomment-667137301
    Let me see if I can backport gcc 10.2 to Debian Buster for y'all :-)
    lutfia95
    @lutfia95
    Hi, what is the main changes in minimiser/kmer_hash between seqan3.0 and seqan3.0.2?
    smehringer
    @smehringer

    Hi @lutfia95,
    I think there have been a few edge case fixes for kmer_hash, namely

    • kmer_hash now preserves common_range
    • It now provides a size() member function if the underlying range is sized
    • If the underlying range is too small for a full kmer, the resulting view is empty

    Also note that the kmer_hash may have returned wrong values due to precision errors of std::pow casting its value to double. We fixed that with our own implementation of pow for integrals.

    Minimizers were just recently added so this a a new feature all together. We provide two views:

    • seqan3::views::minimiser
    • seqan3::views::minimiser_hash
      The second does kmer hashing of the forwward and reverse strand, as well as the minimiser computation in one.
    Ahmad lutfi
    @ah_ol_twitter
    Ok thank you very much
    Michael R. Crusoe
    @mr-c
    My dear German colleagues. I'm having a diffult time navigating http://oeffentlicher-dienst.info/tv-l/ ; my goal is to discover what the exact requirements are for each wage classification from E9 and up.
    Any assistance would be very appreciated!
    I found http://oeffentlicher-dienst.info/tv-l/allg/entgeltgruppen.html but it is still vague and imprecise
    Michael R. Crusoe
    @mr-c
    Some progress, I have found the description of the pay grades at http://oeffentlicher-dienst.info/pdf/tv-l/tv-l-nr11-anlage-a.pdf
    2 replies
    Michael R. Crusoe
    @mr-c
    Should I test a new "release candidate" for Debian?
    7 replies
    Michael R. Crusoe
    @mr-c
    Any help with the post-installation test cmake errors with 3.0.2 is appreciated: https://gitter.im/seqan/Lobby?at=5f723fb1b8a99f4519b270a0
    Michael R. Crusoe
    @mr-c
    Ah, seems like copying over the test/cmake directory fixes that
    1 reply
    Hannes Hauswedell
    @h-2
    Hi everyone! Since I am not up to date with current conventions: where do discussion points go that are not immediate tasks? Do I create an issue at seqan/seqan3 for them or are other places designated for this? There are quite a few issues associated with building/running the tests on a machine without internet. I would like to gather these points somewhere.
    3 replies
    Hannes Hauswedell
    @h-2
    Has someone successfully built our test suite with CMake-3.17? Because I am getting A LOT of errors.
    9 replies
    Michael R. Crusoe
    @mr-c
    Debian is having problems with the seqan3 tests timing out on arm64. Right now we compile + run the unit, header, snippet, and performance tests; which of theses groups of tests can we safely skip?
    2 replies
    Hannes Hauswedell
    @h-2
    Hm, why doesn't our I/O use our fast streambuf iterators?
    7 replies
    Lydia Buntrock
    @Irallia
    Do you know a tool with which you can manage references.
    More precisely: I would like to be able to see how often a paper I have read is cited in the other papers I have read. And I want to be able to see which authors are authors of several papers I have read. So that I can have a kind of relevance assessment for myself and my topic.
    I've tried JabRef, but you can't even include the references of the papers.
    rrahn
    @rrahn
    Not sure if it fits your purpose but I am using Mendeley.
    15 replies
    Michael R. Crusoe
    @mr-c
    Maybe someone wants to add seqan3 to https://github.com/rigtorp/awesome-modern-cpp ?
    4 replies
    rrahn
    @rrahn

    :tada: SeqAn 3.0.2 is released :tada:

    We are happy and proud to announce the new release of our modern c++ library for sequence analysis. Find out more about it https://seqan.de/seqan-3-0-2-release/ or check it out right away https://github.com/seqan/seqan3/releases/tag/3.0.2. Many thanks to all contributors and supporters.

    Michael R. Crusoe
    @mr-c
    Seqan 3.0.2 is in Debian, but I'm having issues with the arm64 build timing out. Is there a subset of the tests I could use that isn't so intensive to compile?
    This is the post-installation script that needs to be modified for Debian https://salsa.debian.org/med-team/seqan3/-/blob/master/debian/tests/run-tests#L26
    Michael R. Crusoe
    @mr-c
    Speaking of celebrations, I finally got a normal residence card! https://twitter.com/__crusoe/status/1316364807205990400
    7 replies
    Michael R. Crusoe
    @mr-c
    This message was deleted
    Hannes Hauswedell
    @h-2
    Is someone at FU tomorrow? There is some stuff in my old office that could be picked up then.
    3 replies
    Michael R. Crusoe
    @mr-c
    Has anyone released a seqan3 based app yet? Or is that waiting for Seqan3 3.1.0?
    6 replies
    Michael R. Crusoe
    @mr-c
    FYI, travis-ci.org is closing down next month. Someone needs to go to https://travis-ci.com/organizations/seqan/migrate to migrate seqan3 to travis-ci.com
    Hannes Hauswedell
    @h-2
    seqan.de is down.
    12 replies
    simonsasse
    @simonsasse
    seqan.de is up and running again. There was an issue with a caching plugIn.
    1 reply
    smehringer
    @smehringer
    :tada: Noice
    Michael R. Crusoe
    @mr-c
    I just learned about the German Employee Inventions Act (ArbnErfG) ; seems like a barrier to Free / Open Science. Maybe @h-2 or others have some advice or opinions to share..
    4 replies
    Marcel
    @marehr
    Funny and short lightning talk about refactoring code (https://www.youtube.com/watch?v=fzmjXK9JZ9o); @rrahn right?
    2 replies
    Michael R. Crusoe
    @mr-c
    Lamda2 doesn't build with GCC 10 anymore https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=975142
    2 replies
    Hannes Hauswedell
    @h-2
    Thank you all again for the wonderful digital hat and for being at the defence :)
    5 replies
    The package builds and the in-tree tests work, but the post installation tests fail:
     export SEQAN3_NO_VERSION_CHECK=1
    + cp --recursive /tmp/autopkgtest.o3QzSs/tree/test/unit ./
    + cp --recursive /tmp/autopkgtest.o3QzSs/tree/test/include ./
    + cp --recursive /tmp/autopkgtest.o3QzSs/tree/test/snippet ./
    + cp --recursive /tmp/autopkgtest.o3QzSs/tree/test/header ./
    + cp /tmp/autopkgtest.o3QzSs/tree/LICENSE.md ./
    + cp /tmp/autopkgtest.o3QzSs/tree/test/seqan3-test.cmake ./
    + mkdir build_unit
    + cd build_unit
    + CMAKE_PREFIX_PATH=/usr/share/cmake cmake ../unit -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON
    -- The CXX compiler identification is GNU 10.2.0
    -- Detecting CXX compiler ABI info
    -- Detecting CXX compiler ABI info - done
    -- Check for working CXX compiler: /usr/bin/c++ - skipped
    -- Detecting CXX compile features
    -- Detecting CXX compile features - done
    -- Finding SeqAn3 and checking requirements:
    --   SeqAn3 include dir found:   /usr/include
    --     …adding submodule include:  /usr/include/seqan3/submodules/sdsl-lite/include
    --   C++ Standard-17 support:    via -std=c++17
    --   C++ Concepts support:       via -std=c++20
    --   C++ Filesystem header:      <filesystem>
    --   C++ Filesystem library:     builtin
    -- Check if compiler accepts -pthread
    -- Check if compiler accepts -pthread - yes
    --   Thread support:             via -pthread
    --   Required dependency:        Range-V3 found.
    --   Required dependency:        SDSL found.
    --   Optional dependency:        Cereal found.
    --   Optional dependency:        Lemon not found.
    --   Optional dependency:        ZLIB-1.2.11 found.
    --   Optional dependency:        BZip2-1.0.8 found.
    --   Optional dependency:        libexecinfo found.
    --   SeqAn3 platform.hpp build:  passed.
    -- Found SeqAn3: /usr/include  
    CMake Error at /tmp/autopkgtest.o3QzSs/autopkgtest_tmp/seqan3-test.cmake:104 (include):
      include could not find load file:
    
        seqan3_test_component
    Call Stack (most recent call first):
      CMakeLists.txt:11 (include)
    
    
    CMake Error at /tmp/autopkgtest.o3QzSs/autopkgtest_tmp/seqan3-test.cmake:105 (include):
      include could not find load file:
    
        seqan3_test_files
    Call Stack (most recent call first):
      CMakeLists.txt:11 (include)
    
    
    CMake Error at /tmp/autopkgtest.o3QzSs/autopkgtest_tmp/seqan3-test.cmake:106 (include):
      include could not find load file:
    
        seqan3_require_ccache
    Call Stack (most recent call first):
      CMakeLists.txt:11 (include)
    
    
    CMake Error at /tmp/autopkgtest.o3QzSs/autopkgtest_tmp/seqan3-test.cmake:107 (include):
      include could not find load file:
    
        seqan3_require_benchmark
    Call Stack (most recent call first):
      CMakeLists.txt:11 (include)
    
    
    CMake Error at /tmp/autopkgtest.o3QzSs/autopkgtest_tmp/seqan3-test.cmake:108 (include):
      include could not find load file:
    
        seqan3_require_test
    Call Stack (most recent call first):
      CMakeLists.txt:11 (include)
    
    
    CMake Error at /tmp/autopkgtest.o3QzSs/autopkgtest_tmp/seqan3-test.cmake:109 (include):
      include could not find load file:
    
        add_subdirectories
    Call Stack (most recent call first):
      CMakeLists.txt:11 (include)
    
    
    CMake Error at CMakeLists.txt:34 (seqan3_require_ccache):
      Unknown CMake command "seqan3_require_ccache".
    
    
    -- Configuring incomplete, errors occurred!