James Bonfield

Climate crisis: We’ve filed our challenge to Starmer’s delay | Good Law Project Global heating is all around us and the government isn’t doing enough – so we’re taking them to court

⚖️🌎 BIG NEWS THIS WEEK 🌍⚖️
https://goodlaw.social/kxzk

GitHub - markmoxon/the-sentinel-source-code-bbc-micro: Fully documented and annotated source code for The Sentinel on the BBC Micro Fully documented and annotated source code for The Sentinel on the BBC Micro - markmoxon/the-sentinel-source-code-bbc-micro

I am delighted to announce the release of my latest project:

Fully documented source code for The Sentinel, Geoff Crammond’s 1986 masterpiece.

Here’s the repository; deep dives coming soon.

See thread for details.

1/9

github.com/markmoxon/th...

#retrocomputing #retrogaming #bbcmicro #c64 #8bit

Happy New Year Kavey

UK ministers urged to cap political donations to ‘rebuild voter confidence’ Letter from 19 organisations says a cap would help to protect democracy, weeks after £9m donation to Reform UK

How about we get rid of political donors all together?
Ban the wealthy elite from owning UK politicians.

Dressed in a Santa suit with snowflakes falling a jolly old elf wrangles a Dune sandworm. (ed. note: meme swiped from @SoDakTruth on Twitter)

@funranium.bsky.social
Always be stealing Dune memes!

SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.

The usual process ofbuilding modern C++ packages from GitHub...

Step 1: download and build yet another new version of cmake.

Bah Humbug. (I tried edited it and no, it did indeed need some new feature. Sigh) I miss the old ways.

A lovely collection of fungi from WildlifeTrustBCN's Gamlingay Woods. #fungi

Never forget: At breakneck speed we are leaving the stable Holocene climate in which human society developed and thrived. Weather extremes are outside historical experience. Sea-level rise is accelerating. Dangerous tipping points are ahead.
Graph: ed-hawkins.github.io/climate-visu...

Spot on with printers though. Satanic devices, and clearly the subject of Rage Against The Machine.

A feeling of dirtiness, a sense of horror, verging on revulsion. So maybe it's a perfect fit for VCF? 🤣

My gut feeling is we'd be better just having a JSON equivalent to VCF than JSON inside VCF. (Eg if we wanted JSON, then the whole of info should be json, not just each element.)

I hear you wish -S. It's not so much that it's not needed, it doesn't harm, but that it's typically indicative of out of date information still doing the rounds/

My pet peeve is "samtools view -b foo.sam > foo.bam" instead of "-o". It causes lots of confusion with nohup and similar.

I've heard that before too, but the naming of it predates my involvement so I've no idea if it stood for anything. It's plausible, but *shrug*.

It's curious to see grokipedia is up and has samtools, SAM and BAM pages all with a flurry of edits. Oddly, most of those edits are correcting minor edits in the Wikipedia pages it based its content on (presumably via some AI rewriting tool).

A shame the originals weren't edited too.

Efficient and accurate search in petabase-scale sequence repositories - Nature MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

You can't out reform Reform. They're loony conspiracy theory nutters - you shouldn't *want* to woo them!

We need parties that accept why the economy has tanked and will take steps to fix it. Leaving the ECM - Common Market - was the dumbiest idea ever (regardless of how you voted on Brexit).

"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary."
engineering.fb.com/2025/10/06/d...

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

Note: OLD POST! (2023), but I just noticed it.

While it's nice to see comparisons, why compare an (at the time) 2 year old GATK against a 5 year old bcftools?

Since then both have come on a lot. It'd be interesting to see new independent comparisons. (Neither can hold up to deepvariant now.)

I noted in their presentation they said that samtools mpileup didn't work. I think they're a bit out of date. Bcftools mpileup --poly-mqual can handle the qualities in homopolymers, plus other newer -X profiles.

I haven't tuned it yet though for SBX, but think it'll be OK in general. (To try!)

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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.

Instagram is like facebork but even more annoying. I looked and I can't even find the equivalent post for you over there. It's just a hateful platform. Probably OK for doom scrolling on a phone, but that's about it.

We ought to update htslib.org with more precise recipes, especially for things like conda where we know A) people make mistakes, often and B) it's used A LOT. We may be able to point to something like biocontainers too (or roll our own, but I'd rather not).

It's rarely built from source it seems.

Even more prolific is looking at their WhatsApp number from the minimap2 fake site, and associated email. So so many fake sites. Scary

(See 447950904740 phone number, and emmawatsofficial54 partial email search results).

A google for the support phone number shows how many other phishing sites they have.

www.google.com/search?clien...

Most likely their "support" offering involves getting you to install some trojan.

Phishing site : minimap2.com · Issue #1316 · lh3/minimap2 Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...

minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...

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

Nothing like cold hard data. It's almost as if Brexit was a pack of lies? Who'd have believed it. ;-)

Of course the people that need to see this obviously won't as it'll be deemed "fake news". I really don't know how to fix that one.

Nigel Farage looks uncomfortable as Jamie Raskin uses his opening statement to absolutely demolish him