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    Marcel
    @marehr
    A pretty cool article for computer scientists regarding RNA/DNA/amino acids and how they work in a language understandable to them xD https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/
    Knut Reinert
    @kreinert
    @smehringer Kommst du zum Interview?
    Ahmad lutfi
    @ah_ol_twitter
    Hi Folks, is there any implementation of Q-gram index in SeqAn 3 ?
    1 reply
    Ahmad lutfi
    @ah_ol_twitter
    Thanks for the answer, I would like to use q-gram for the similarity search between reference genome and sequencing data. I am trying now if the FM-Index is more efficient than q-gram.
    1 reply
    Michael R. Crusoe
    @mr-c

    I know that Seqan 1.x is basically unmaintained, but we did get a significant looking set of test failures with gcc 10: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=980685 We only have one application in Debian that uses Seqan 1.x (dindel) and it is dead/archived by its authors.

    The likely outcome is that both dindel and seqan 1.4.x will not be in the next release of Debian unless someone wants to fix the test failures.

    4 replies
    Hannes Hauswedell
    @h-2
    Just a thing I stumbled upon: Is there a reason some of the meta info of the arg parser is a vector of strings?
    6 replies
    Hannes Hauswedell
    @h-2
    I know there is no clang support, yet, but has someone already tried making a clang-format file for the style currently used in SeqAn3?
    16 replies
    Hannes Hauswedell
    @h-2
    In case you haven't seen this, it may be quite useful:
    https://cppinsights.io/s/f07eed7b
    [Maybe collecting such ressources for new contributers would be good? We used to have Wiki-pages on Modern C++]
    Hannes Hauswedell
    @h-2
    SeqAn3 switched to Github-actions, right? Is travis completely dead? And do you recommend we switch Lambda to Github actions, as well?
    4 replies
    Chris Bielow
    @cbielow
    good day everyone. I hope this is the place to ask this:
    Are there any benchmarks for proteomics data which compare the FM-Index implementations of Seqan2 vs Seqan3? Which one is faster?
    Hannes Hauswedell
    @h-2
    I have done extensive benchmarking with protein data in lambda. Currently the FM-Index in SeqAn2 is significantly faster. There are patches that bring SeqAn3 closer to SeqAn2: xxsds/sdsl-lite#75
    Chris Bielow
    @cbielow
    ok, thanks!
    On another note: I was hoping to query peptide sequences against proteins which may contain ambiguous amino acids (like J for I or L), without allowing for actual mismatches. I have not looked into the code, but I though it might be possible by selecting the correct ranks for amino acids and defining a custom equality operator...
    Hannes Hauswedell
    @h-2
    What do you mean my "selecting the correct ranks"? Why not just write a function bool my_compare(aa27 lhs, aa27 rhs) with the desired behaviour?
    Michael R. Crusoe
    @mr-c
    The website is down? https://www.seqan.de/
    1 reply
    seqan/seqan#2458
    Joshua Kim
    @joshuak94

    Helloooo. I'm struggling a bit with getting a random position in a random chromosome from an indexed BAM file, could somebody help me out? Here's what I've currently got:

    using my_fields = seqan3::fields<seqan3::field::ref_id,
                                     seqan3::field::ref_offset,
                                     seqan3::field::cigar>;

seqan3::alignment_file_input alignment_file{alignment_file_path, my_fields{}};

uint8_t num_chr = alignment_file.header().ref_ids().size();

uint8_t rand_chr = rand() % (num_chr + 1);
uint64_t rand_pos = ???

    I'm just not too sure how to use ref_id_info and ref_dict with what I have above... I guess std::get<0>(ref_id_info) with the appropriate seqan3::field::ref_id should give me the length of the chromosome, but I don't know how to get this.

    17 replies
    Joshua Kim
    @joshuak94
    Just kidding, I figured it out!
    Joshua Kim
    @joshuak94
    Getting this weird bug: seqan/seqan3#2417 does anybody know about it?
    Joshua Kim
    @joshuak94
    Can somebody confirm: Records in seqan3, are they 0 based half open half closed or are the 1 based closed intervals?
    SAM format is 1 based and closed intervals, whereas BAM files are 0 based half open half closed. But when the alignment_file_input parses these records, which way are they converted?
    Enrico Seiler
    @eseiler
    We always do 0-based, i.e. we subtract 1 from the positions in the SAM file
    Michael R. Crusoe
    @mr-c
    Does Seqan do much string parsing to pull out numbers? biojppm/rapidyaml#40
    2 replies
    → https://github.com/biojppm/fast_float
    Hannes Hauswedell
    @h-2
    Doxygen has experimental support for concepts: https://github.com/doxygen/doxygen/issues/2732#issuecomment-816095669
    2 replies