When you think the cloud looks low because of the horizon but then: Sky Tower

VG will soon start adding headers to the GAF files it generates. The specifics are still uncertain, but if you maintain a GAF parser, it may be a good idea to skip lines starting with "@". Here is a draft specification for the vg flavor of GAF.

October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2 Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.

BTW @jbonfield.bsky.social someone edited Wikipedia's CRAM page a while back to add the unreferenced claim that it stands for Compressed Reference-oriented Alignment Map. Citation needed! As I recall, it officially doesn't stand for anything but is merely reminiscent of compression and references…

Okay, for the folks who asked: here's the majority AI view, writing up the reasonable, thoughtful view on AI that the vast majority of people in tech hold, that gets overshadowed by the bluster and hype of the tycoons trying to shill their nonsense. anildash.com/2025/10/17/t... Please share!

Hard to believe how much damage SemVer has done to people’s brains.

A file format specification (hopefully!) spells out what's valid and invalid. Implementations have choices for how they deal with variously out-of-spec files: • reject with error message • reject mysteriously • accept as an extension, with a well-defined meaning • accept mysteriously • crash • …

If you ever submit on bills, read legislation on legislation.govt.nz or use its RSS feeds to keep track of new bills, please tell the Parliamentary Counsel Office to make sure the new site keeps RSS. We shouldn't need to have an API key. Fill in the survey: www.legislation.govt.nz/news.aspx#rs...

Genomics for Aotearoa New Zealand - Public Webinar 14th October @nicrawlencenz.bsky.social will be giving a public webinar on myth busting de-exctinction. The webinar will run from 11:00 am to 12:30 pm including time for questions. Please boost this to help reach a broad audience. 🙏

Wonderful news. A salutary reminder of the absolute benefits of scientific progress, and the absolute evil of conspiracist bollocks. Huntington's disease successfully treated for first time www.bbc.com/news/article...

I'm sorry, worldwide, irrevocable, non-exclusive, transferable permission to my voice and likeness? For what now? In any manner for any purpose??? This is in academia/.edu's new ToS, which you're prompted to agree to on login. Anyway I'll be jumping ship. You can find my stuff at hcommons.org.

A modest proposal: Unsuccessful InternetNZ electoral candidates should post to NetHub only in proportion to the percentage of votes they received.

Is there anyone here at one of the universities in Wellington, NZ, who would want to host me to give a talk around November 10th?

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

Submitted on the Electoral Amendment Bill with 3 minutes to spare! Was reminded at the last minute that this bill has another go at disenfranchising prisoners (as has been shot down in the courts repeatedly)… so forgot to say that the deadline change likely won't speed up getting results anyway. 🫠

Watching talks on CMake while working out. I truly appreciate the work folks put in to keep trying to explain the "modern" CMake way. But in every case, I quit watching in disgust. CMake is an example of how to do everything wrong, and when cutting your losses is the best course of action.

Naively assumed that with the #InternetNZ election over, we wouldn't be hearing from the spaceman again. But I haven't been back there for long; perhaps he's been invested in spamming them with the same opinion over and over for longer than I realise…

We have endless browser and html extensions, but it maddens me that no one made a common ISP-level protocol to query datacaps that returns: - Monthly quota (if any) - Current usage (bytes used) - Reset date/time - Throttling policy (what happens when you hit the cap)

Americans, I am once again begging you to consider that sometimes people aren't in America and may be discussing their own bad governments on the niche microblogging website. Please. I am begging.

Pleased that Debian 13 "trixie" has now been released. Prior to this, by my reckoning Debian was the only remaining major platform that did not package Cython 3.x in its system package repositories. With Cython 3 available everywhere, pysam can reasonably require it and simplify a few things.

“Why are you so mindbogglingly pedantic about not using identifiers in the compiler's reserved namespace, John?” (Not sure how the reporter has managed to get the Linux kernel version of <ctype.h> though. Or some other header that similarly defines _P.)

You can lead an open-source maintainer to water (provide a minimal test file exhibiting your bug, already named according to the style of their existing test files), but you can't make them drink (incorporate the new test case into their test suite).

If someone wanted to pay me to give bioinformatics format specifications the time and attention they deserve, I would be very pleased. Otherwise, the work occurs as academic generosity in odd hours by people who are already oversubscribed in their day jobs.

For what it's worth, some thoughts on the member motions for tonight's InternetNZ AGM from one of this year's influx of new INZ members. Unfortunately I wasn't there for most of the recent InternetNZ history and context, but nonetheless I have some reckons… 😀 TL;DR I'll be voting NO on all of them.

Note to self: Don't start writing a submission an hour before the deadline when your internet is in and out due to a storm (presumably). Oh well… bit more crap than planned and I couldn't find a reference for the UK's use-your-MPs-face.com age verification dodge, so no footnotes for that paragraph.

TIL Python's print() function has a flush=True argument that flushes the output stream after the rest of the arguments have been printed. Thus obviating the need for a separate sys.stdout.flush() in many cases.

After 30+ NetHub messages almost entirely on non-technical topics, it seems one of our new InternetNZ members (so new he was late enough to the kerfuffle that he can’t yet vote) has rage-quit. I can only hope that I contributed in some small way to this situation.

With Tom Lehrer's passing, I suppose this is a moment to share the story of the prank he played on the National Security Agency, and how it went undiscovered for nearly 60 years.

As predicted ... here is the NZBORA s7 report on the Government's Electoral Amendment Bill, in which the removal of same-day enrolment and voting for the entire advance voting period is declared to be an unjustifiable limit on the right to vote.

I'm probably motivated to write up some thoughts on several motions for the upcoming InternetNZ AGM. There's some scope for light rather than heat even on their NetHub slack instance. OTOH adhering to a policy of “do not engage with the racists” is getting a workout on some of those NetHub threads…

@tomtomorrow.bsky.social @rubenbolling.bsky.social First they come for the comedians, then the cartoonist. Kings fear being laughed at. We have a funny bone to pick with/without a smile on our faces #Colbert #Kimmel #SethMeyers #DailyShow

If only he had a really famous quote from this show that illustrates this swerve into disappointment

A chance encounter threw me into the campaign to expose the police killing of Jean Charles de Menezes. What happened next changed my life

Release 1.22.1 of HTSlib and SAMtools is now available from GitHub. This fixes crashes that could happen when reading malformed CRAM files, or when writing files with very long secondary alignments as CRAM 3.1. See htslib.org/download/ for links to tarballs and release notes.

As steward of the .nz domain, InternetNZ's governance directly affects the resilience & accessibility of our Internet. As a charity, its good works promote a fair, inclusive, and accessible Internet. This year’s board election is one of the most important in the org's history, and we need your help.

If the MPs are too busy in their electorates for ANY of them to be present in the Wellington #RSB committee room, maybe the staff could put a screen in front of the submitters beside the camera. Many submitters understandably looking off to the side wall at the people on screen instead of to camera.

For many of those who were asking on BLOW5 vs POD5 for nanopore signal data, here is a finally detailed benchmark we did: biorxiv.org/content/10.1... Summary: performance of BLOW5 is >= POD5 (from ~= to 100X, see below), with benefit of having ~3 dependencies instead of >50.

This actually happened news.uga.edu/new-fungal-v...

I love that 'repo' is te reo for 'swamp'

❤️❤️ Thank you, Aotearoa! ❤️❤️ 🗣 Submissions on the Regulatory Standards Bill are now closed. To every single person who stood up, spoke out, and made their voice heard - ngā mihi. This is people power in action. You lift us. We’ll keep you updated on what comes next. #TeTiriti #RSB #NZPol

Regulatory Standards Bill submission sent. I only focussed on one aspect; reading RSB postings here reminded me of others I care about, but the TPB process left such a bad taste that I didn't want to spend long on this one. It'll be tallied, and the aim is to show there's no mandate for this trash.

🍿 github.com/samtools/bcf...

It's actually funny how dedicated the samtools & bcftools maintainers are to their policy of “Conda is unknowable magic. We have failed many times trying to install something with it ourselves”. 🤣 github.com/samtools/bcf...

I'm feeling this very strongly this morning, as an issue I filed saying “We believe [a crash] is fixed by [PR#nnn]. However there are additional bugs in this background task that are not addressed by that PR: [bullet list]”… …has just been closed “We also believe this has been fixed by [PR#nnn]”. 🙄

We had to work around changed enum behaviour in Cython 3.1.1 not long before the previous pysam release, and now we have to work around an unfortunate trivial bug in Cython 3.1.2. Apparently we need to start testing building pysam with pre-release Cythons… github.com/pysam-develo...

Foolishly I hadn't given my #MWSecretSantaAoNZ person any hints as to suitable gifts, but they've done spectacularly well nonetheless. My partner and I have one pair of binoculars for watching birds and other wildlife, so a second little pair so we can both look at once is perfect. …

Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪 #samtools #bcftools #htslib #bioinformatics

Government by Illiterate Chode