Second post about Seqair, my #rustlang take on htslib. This one is about streaming VCF/BCF writing and type-state/session type APIs! #bioinformatics

okay so i thought it is really cool how kroki.io has a public api to render diagrams i can call it from hugo templates. but now the api is down and i can't post to my blog because ci needs to call that api to get the diagrams… time to build a cache

One more #rustlang post! This time on niches for integer ranges using pattern types on nightly!

Was contemplating posting the seqair article over the May 1st weekend, assuming nobody would have a look and I’ll just have to repost on Monday/Tuesday. I was wrong :D

If you're leaving GitHub, we'd be very happy to chat! We work remotely, pay top-end of European salaries and are hell bent on building the best code forge ever. We're hiring for one intermediate/senior role right now: jobs.tangled.org/software-eng.... Go, Firecracker, distributed systems.

Seqair, my Rust-native take on htslib

I spent some time writing about a #rust library I've been working on: seqair, an alternative to (a subset of) htslib. This is a big one! So much potential API surface to cover and I better have a good reason for it! deterministic.space/seqair.html

I was about to write a blog post after having done some research here but I see everyone already published that post today

Still blogging

The best kind of blog posts about blog tooling and blog redesigning, right?

What’s the latest in git hosting? Saw @tangled.org and codeberg.org and also lubeno.dev and I’m happy to see movement in the area. Did I miss anything? What do people think about that?

Wow, kroki.io is pretty awesome to include diagrams as svg in hugo! and with enough `!important`, it even works well with dark mode

Random Forest ML on GPU deterministic.space/gpu-random-f...

Claude Opus 4.7 has a great time not detecting malware I see > This is a SAM/BAM base-modification tag parser — a bioinformatics file format library, not malware. The user asked for a spec review, which is analysis (not augmentation), so I'll proceed with the review report.

So bsky doesn’t load for me because “api.pop1.bsky.app is down” but I can just open blacksky and log in and it works mostly? Is this a decentralization test?

Using CSS vars to style SVG symbols

After writing one article I finally also had the motivation to do the redesign for @deterministic.space that I’ve wanted to do for years (including dark mode!). And now this is done and it’s fresh and nice I also haven even more motivation to write

Notes on Rastair, a variant and methylation caller

Finally wrote a post about the project I’ve been working on! And gave my blog an account

Not sure this is on purpose but I just found a new business model for myself

⚠️ An active phishing attack is targeting crate owners by asking them to "confirm that your email address is still active". These messages are not from crates.io, and should be ignored. (We will never ask you to confirm that your e-mail address is still active.) ⚠️

Finally, I'm writing file readers and have an excuse to use fuzzers again!

Rastair: an integrated variant and methylation caller https://www.biorxiv.org/content/10.64898/2026.03.19.712983v1

🎉New preprint out today! We present rastair - an ultra-fast SNP and methylation caller for TAPS or 5-Base data. Rastair takes less than 1h to process e.g. a 50x 5-Base dataset, yet SNP call accuracy is nearly identical to GATK on WGS data 🔥

Just forked github.com/Softleif/cstr8 to add compact (≤22bytes inlined) null-terminated utf8 string that can be passed from #rust to C (and vice versa). I bet there are other libraries that do this better, right?

A bit more than a month after 2.1, we now released Rastair 2.1, a #rust tool that detects variants and methylated positions from TAPS and 5base sequence reads. 2.1 adds GPU support and a bunch of other performance optimizations that I'm quite proud of! www.rastair.com

I’ve reached the state where I’m just adding more and more features to all the forks I’m maintaining because it’s fun and easy. Next, talking with the maintainers how I can actually upstream all of it 😅

Saw a bunch of talk about @fasterthanli.me’s tracey.bearcove.eu and now also @dollspace.gay’s forecast.bio/crosslink/ and both look interesting and like they should be combined!

Last week, I was working on one of the fastest tools in its category. Then I got tricked into optimizing it, made Claude write some compute shaders for me, got rid of more `memmove`s, and now I think I can run on laptop in 10min what last week ran for 2.5h on a server with 16 cores! #rustlang

Is it weird that I as a human have more fun reading skill files compared to actual programming books?

@fasterthanli.me what ever happened to your experiments/research into with writing specs with ids and then tracing them in the code? I remember seeing you post about it and I think @jamesmunns.com and you talked about it but can’t find it anymore :)

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🦀 A unique #opportunity for #RustLang enthusiasts and verification researchers: Join us for a three-year project formalizing a Rust subset – and pursue a PhD if you choose. Interested? 👉 ferrous-systems.com/blog/researc...

In case anyone else needs to hear it: `Vec::with_capacity(user_input)` is probably a bad idea and will eat your RAM when you least expect it. At least put a `.min(reasonable_max)` on it. #rust

Fellow #rust and #lldb users, how hard is it to add support for some common library types like SmallVec or SmolStr? I want to inspect my nice inlined types!

It's time for the State of Rust Survey! The Rust Project invites you to take this year’s survey, whether you have just begun using Rust, you consider yourself an intermediate to advanced user, or you have not yet used Rust but intend to one day 🦀

A bunch of folks at Oxide uncovered a tricky deadlock associated with async Rust (yes, another!), so--of [email protected] and I got the crew together to discuss. If you're writing async Rust, you'll want to know how to avoid and diagnose "Futurelock"

Been reading up on the source of one of my fav quotes (~”don’t attribute malice to what can be explained by stupidity”) by reading quoteinvestigator.com/2016/12/30/n... — how’s your Saturday going?

There are only a few projects whose release notes excite me and @typst.app is one of them

What's this pattern in #rustlang called, where you use a block to initialize a variable? I use it all the time

I am looking to get my hands on some #Illumina 5-base methylation data - does anyone have a bam file that I could use for some testing? Please RT for reach!

At #EuroRust and picking the talks about stuff I would never look into otherwise :) cosmic was interesting and now learning about Petri nets

Going to @eurorust this week! Been a while since I’ve been to a rust conference, looking forward to it :)

Wrote a blog post about this, I thought it was quite interesting https://deterministic.space/bufwriter-lz4.html

I wrote a blog post about fiddling with buffered LZ4 writers in #rustlang deterministic.space/bufwriter-lz...

Random #rustlang insight: A `BufWriter<lz4::Encoder<File>>` is faster than `lz4::Encoder<BufWriter<File>>` for me when serializing many small structs. Super easy to swap around but only came up with it after looking at a flamegraph

I needed a "reasonable" debug file format in #rustlang so 1h later I have serde, message pack, and LZ4. And another hour later, I have tricked it into reading a stream of message pack documents out again

Please share: I'm still looking for a postdoc in computational genomics to join my team in Oxford. If you want to help develop better ways to detect AML from epigenetic profiles in blood, then get in touch! Great team and environment, 3-year secured funding, ideal for transition to independence.

That looks like a really cool job! I’ll be looking for contracting jobs from September again, but this is tempting!