Rastair: an integrated variant and methylation caller www.biorxiv.org/content/10.64898/2026.03...

As a software engineer who loves to design systems for the craft of it and also uses AI tools (as tools not replacement for thinking), I agree very much and would love there to be a positive future where software can be good and help people (not just investors/shareholders)

Can set a cargo alias for t/test or is cargo gonna complain?

🎉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 🔥

One curious thing I noticed is that in the European morning it’s was faster and subjectively smarter/more efficient. And then after lunch time here you feel the US starting their day.

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?

I'm not good with numbers, lol. *2.0* was on Feb 8, *2.1* now.

Would be cool to do more on that front, because I see a bunch of opportunities! All I need is someone to sponsor me for a couple days per month to be able to prioritize this :)

Softleif Softleif has 7 repositories available. Follow their code on GitHub.

Along the way, I also forked a couple of our major #bioinformatics #rust dependencies to github.com/orgs/Softlei... with the biggest one being rust-htslib where I added a bunch of stuff and tried to make it more Rust-y

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 😅

Oh I just saw you updated the bgzf crate and now I see you on here as well! Thanks for that :)

It’s fun! Had some good results with a skill describing how to quickly find stuff in the docs for the project (md files) but not really with having Claude update the same docs automatically

Congrats! I hope it’s gonna be a fair 50-50 split between embedded rust and podcasting!

(Also the another thing missing for me is having time and a reason to use either lol)

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!

Would be neat! Or json.get(“data”, 1, “id”) with tuple magic

Either give [] indexing syntax some actually good features (like return options easily, tuple overloading, etc. to allow `json[“data”, 1, “id”]`) or get rid of it and have generics use brackets!

only using rust myself, too, but not seen any crashes

This is something I should write a blog post about as well… but for now, if you're curious check out www.rastair.com and its repo where this is happening :)

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

So many opinions on this one. Zoomable graphs with different levels of details showing summaries makes perfect sense to me cause that’s what it oooks like in my head (maybe also buy a 50” touch screen but that’s an easy fix)

Advanced data visualization in Typst − Lilaq Advanced data visualization in Typst

Very cool! Was looking at lilaq.org recently based on Typst (makes it quite flexible for the cost of learning and bundling typst) but this looks even more feature-full :O

Fun to read in this format too! I kinda liked the big GitHub link previews as visual dividers but that’s a minor thing. Your *this* close to just making a “this week in bevy merge train” blog aren’t you?

oh yes! i love that format

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

GitHub - wolfpld/tracy: Frame profiler Frame profiler. Contribute to wolfpld/tracy development by creating an account on GitHub.

Oh hahaha I saw this name and for some reason thought it was related to tokio-tracing or github.com/wolfpld/tracy

@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 :)

Ah, neat! Always cool to see you do new stuff in the space. Might finally have a use case for facet soon with cli/config files/docs generation :)

Woah another facet thing going in another direction? I have a hard time keeping up 😅 need to make time to read a couple weeks worth of your posts!