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    Ciarán O'Mara
    @CiaranOMara
    I really like the electrostatic examples.
    Young Jae Woo
    @youngjaewoo
    Thank you for the biomart in julia! Very excited.
    Kevin Bonham
    @kescobo
    @BenJWard you ready to take a look at logs? Gonna try to bump version on BiobakeryUtils
    Waiting for CI to finish here: BioJulia/BiobakeryUtils.jl@fa35517
    Gonna go work on my fence, but back in ~10 min
    Kevin Bonham
    @kescobo
    Just kicked it off
    Kevin Bonham
    @kescobo
    Still hasn't triggered :-(
    Ben J. Ward
    @BenJWard
    Hey @kescobo can you try it again? I'm back behind my laptop properly now.
    And I have the log page open so I should catch it
    Kevin Bonham
    @kescobo
    @BenJWard OK, doing it in ~30 sec
    Ben J. Ward
    @BenJWard
    :+1:
    Ben J. Ward
    @BenJWard
    Ok it's responding
    waking up
    Ben J. Ward
    @BenJWard
    Hmm
    So it looks like it's seeing you call it
    And the request get's sent
    But it seems to respond saying 204 - DONE! without actually doing anything
    So I probably need to first check the HTTP payloads sent by myself or Ciaran and those sent by you to see if there are any significant parameter differences.
    Kevin Bonham
    @kescobo
    Lol, like I said, BioJuliaBot hates me...
    Ben J. Ward
    @BenJWard
    And I'll check Registrator code as well to see if there's some decision it takes to just respond 204 without doing anything
    Kevin Bonham
    @kescobo
    :thumbsup:
    And while you're at it, almost certainly unrelated, but I'd love your thoughts on this: BioJulia/BioJuliaRegistry#53
    Anyone else feel free to chime in too
    Ben J. Ward
    @BenJWard
    Ok I'll have a think about that.
    Ben J. Ward
    @BenJWard
    @kescobo So one thing that is interesting... in my json payload when I commented it says: @BioJuliaBot register... for yours it says @biojuliabot register... Here's my idea what's happening - may be wrong, maybe not: So I think if you or anyone enters @biojuliabot register, whilst GitHub will recognize you're using BioJuliaBot's handle and will capitalize it for you when it renders your comment - Registrator is far more literal, and when the comment data arrives in the HTTP payload, it's like "@biojuliabot? Who's that? I'm listening for @BioJuliaBot!" ... and so it's ignoring you until you capitalize it's name!
    Kevin Bonham
    @kescobo
    Lol, k
    I've definitely been putting it in lowercase
    Ben J. Ward
    @BenJWard

    Yep ok here's the relevant registrator code:

    trigger = Regex(CONFIG["trigger"] * "(.*)")
        listener = GitHub.CommentListener(comment_handler, trigger; check_collab=false, auth=auth, secret=CONFIG["github"]["secret"])

    So the trigger is a regex of the exact trigger phrase (@BioJuliaBot register) followed by any other text, so it's gonna be sniffy about the caps!

    Although you know this suggests editing the trigger string in the config might be able to get it to recognize the lowercase from of the name
    Kevin Bonham
    @kescobo
    @BenJWard Very interesting. If we don't care about case at all, then it's as easy as changing it to Regex(CONFIG["trigger"] * "(.*)", "i"). Alternatively, if we only want to allow lower-case in the name, regex could be "^@[Bb]io[Jj]ulia[Bb]ot register"
    Kevin Bonham
    @kescobo
    @BenJWard :heart_eyes: BioJulia/Microbiome.jl@d794830
    Kevin Bonham
    @kescobo
    Hmm - bad news is that now it doesn't seem able to be installed at all https://github.com/BioJulia/BioJuliaRegistry/pull/54/checks?check_run_id=477021230
    All my other packages are broken too
    Ben J. Ward
    @BenJWard
    @kescobo If you want to de-register and re-register the Microbiome - verse then that's ok, just lemme know what you need to get it running.
    Kevin Bonham
    @kescobo
    @BenJWard OK, thanks... fixing stuff in the General registry helped a bunch, but I still think this would be worth doing. I'll plan it out and let you know later this week or early next
    Ciarán O'Mara
    @CiaranOMara
    If anyone here is using XAM.jl v0.2, there is an issue with versions v0.2.0, v0.2.1, v0.2.2 where the in-place record used during the iteration of SAM records was not emptied between iterations. This occurrence means that for successive iterations, record fields not overwritten would contain values from a previous iteration instead of being empty. The release of XAM.jl v0.2.3 addresses this issue.
    mmattocks
    @mmattocks
    BioJulia/BioSequences.jl#110 I thought it was just me but it seems someone else is seeing the same behaviour- reverse_complement mutates sequences. Does anyone have an idea about where to start with this? I kind of need BioSequences to be algorithmically reliable nowish so I am willing to investigate if need be
    Ben J. Ward
    @BenJWard
    Have you tried master? There have been improvements and changes to reverse complement recently that may have ended up fixing your issue. If master works for you all we have to do is get on with cutting a new release, if not, we have some more hunting to do.
    Joe Greener
    @jgreener64
    The BioStructures.jl paper is out in Bioinformatics :boom:
    Kevin Bonham
    @kescobo
    Holy crap! Great work you guys
    Joe Greener
    @jgreener64
    Thanks
    a.v.mantzaris
    @mantzaris
    is the Smith–Waterman algorithm implemented in the package? I cannot find an explicit reference to it in the docs, or is another algorithm implemented which provides similar functionality ?
    Pavel V. Dimens
    @pdimens
    Congrats!
    Ciarán O'Mara
    @CiaranOMara
    Congratulations
    gopi1616
    @gopi1616
    Hi, I am a python programmer and new to Julia. One of the tasks I am working on needs modification of description lines in Fastq sequence files.
    Doing this in python was pretty time-consuming. So wanted to try the same in Julia with FASTX package.
    Can anyone recommend a method or provide an example to loop through each description and substitute with a modified line and writing it back to Fastq in an efficient way?
    Kevin Bonham
    @kescobo
    @gopi1616 I responded over on discourse - it would be helpful to see what you tried