Sign in

Pascal

@killercup.de
103 followers 128 following 144 posts

Freelance Rust nerd Blog: @deterministic.space Pronouns: He/him Location: Sweden

PostsRepliesMedia
Pascal @killercup.de · 02/10/2026
I know there are many of these (I added a list!), but for some reason or another it didn't really fit with how i wanted to use it in rastair. Maybe it's useful for someone else, too!
000
Pascal @killercup.de · 02/10/2026
I released a new small #rust crate that lets you process items in parallel but get them back in order: github.com/Softleif/ord...
github.com
GitHub - Softleif/ordair: A parallel map on a rayon pool whose results reach a sequential consumer in input order, with a hard bound on how far the workers run ahead of it.
A parallel map on a rayon pool whose results reach a sequential consumer in input order, with a hard bound on how far the workers run ahead of it. - Softleif/ordair
122
Pascal @killercup.de · 25/09/2026
Just released seqair 0.3.1 that includes a bunch of SIMD and other performance stuff :) github.com/Softleif/seq... #bioinformatics #rust #simd
github.com
Release seqair 0.3.1 · Softleif/seqair
A performance release. Every hand-written core::arch kernel is now one portable fearless_simd kernel, and the readers, pileup engine, CRAM codecs and writers were profiled and tightened around it. ...
010
Pascal @killercup.de · 24/09/2026
regardless of how you feel about llms, this just made my #bioinformatics #rust code faster while i was having lunch. there are a lot of proptests already for this, so i feel confident this is not gonna break
131
Pascal @killercup.de · 24/09/2026
In seqair I had claude write avx and neon stuff for methods I knew would benefit from this and I didn't want to think about doing it myself. Turns out, claude is also fearlessly using fearless_simd with great results github.com/Softleif/seq...
github.com
fearless simd by killercup · Pull Request #65 · Softleif/seqair
Closes #64
110
Pascal @killercup.de · 24/09/2026
Super awesome release! I previously used `wide` for some SIMD stuff but it didn't really deliver what I (a novice at vector instruction crimes) needed.
180
Pascal @killercup.de · 06/09/2026
Do I have to bring slides?
120
Pascal @killercup.de · 03/09/2026
@skyrdle.com are you down? 😮I finally have time to play again
100
Pascal @killercup.de · 27/08/2026
Very cool! Just yesterday I was finding myself with enough time (while running hap.py) to wonder if someone made a rust version yet. Cool to see your improvements and basepair mode on top!
010
Pascal @killercup.de · 25/08/2026
For the US folks :) #bioinformatics
010
Pascal @killercup.de · 25/08/2026
Next up for me: integrating github.com/Softleif/seq... and supporting phasing
github.com
GitHub - Softleif/seqair: BAM/SAM/CRAM/FASTA reader, pileup engine, BCF/BAM writing
BAM/SAM/CRAM/FASTA reader, pileup engine, BCF/BAM writing - Softleif/seqair
000
Pascal @killercup.de · 25/08/2026
Please give it a try if you're in the field :) Rastair works for both TAPS and 5base, it's really really fast, and even faster if you use `--gpu`! I test this on my laptop and a whole 70x sample is just slow enough enough for a nice coffee break
100
Pascal @killercup.de · 25/08/2026
We also now moved the repo over to github… weird move in 2026, I know, but bitbucket wasn't better and now people can at least file issues a little nicer.
100
Pascal @killercup.de · 25/08/2026
New release of rastair! 2.2.0 is out with a bunch of goodies including calling of indels! github.com/bsbludwig/ra...
github.com
Release v2.2.0 · bsbludwig/rastair
Highlights: The reported beta values might change when updating to rastair 2.2. Methylation beta is now calculated by taking into account both positions of a CpG, meaning only reads containing TG/...
100
Pascal @killercup.de · 06/08/2026
During my summer break, I wanted to build a little app for myself to save article links and read their content. It's a bit more complex. I wrote up my ideas and what my current version does here: deterministic.space/readleif.html
deterministic.space
Readleif
001
Pascal @killercup.de · 28/07/2026
europeancorrespondent.com/en/r/how-… :)
europeancorrespondent.com
How colour drained from our furniture
I
010
Pascal @killercup.de · 17/07/2026
So far I only added what we needed in our use of rastair :) I’ll have a look at FASTQ support when I’m back from vacation
001
Pascal @killercup.de · 26/06/2026
AT Mot 4 (EN) 3/6 🟨⬛🟨⬛🟩 ⬛⬛⬛⬛🟨 🟩🟩🟩🟩🟩 atmot.herve.bzh/p/en/4
atmot.herve.bzh
AT Mot 4 (EN)
A bilingual daily word game on the AT Protocol. Play today’s puzzle.
000
Pascal @killercup.de · 26/06/2026
I scored 793 in moo jump on mu! Can you beat it? hello.mu.social/play/793
hello.mu.social
I scored 793 in moo jump
Can you beat my score on mu?
010
Pascal @killercup.de · 25/06/2026
Mastodon, with account handles having two @s, should immediately follow up and start using "Log in with @@"
140
Pascal @killercup.de · 24/06/2026
Is there any read later app that you use that has good text-to-speech? (Maybe also one that is fast, mobile+desktop, and trustworthy)
100
Pascal @killercup.de · 24/06/2026
Yeah, I totally get that. Sadly also looks more like a translation than a rewrite, with not very idiomatic code. Curious to see what’s gonna happen with it
010
Pascal @killercup.de · 24/06/2026
Yes, i hope it’s not a one-off effort either… I asked since I assumed it would be simpler to add python bindings and make its rust API nicer than to first create bindings :)
100
Pascal @killercup.de · 22/06/2026
Nice! Did you try github.com/henriksson-l... as well?
github.com
GitHub - henriksson-lab/minibwa-rs
Contribute to henriksson-lab/minibwa-rs development by creating an account on GitHub.
110
Pascal @killercup.de · 20/06/2026
I assume this is more powerful but I have no clue how to set up a good template. I’ve been building with debug symbols but also with mimalloc which seems to confuse it a bit… let’s see if I have to dive into this or if there are summary tools for this
110
Pascal @killercup.de · 19/06/2026
If the answer is “you’re on a Mac so use Instruments” please send me a tutorial that makes sense for people who don’t use Xcode :D
100
Pascal @killercup.de · 19/06/2026
I’ve been using samply to profile Rastair, a CPU heavy #rustlang CLI tool (it also has tracing for logs but it’s not async). I’m wondering if someone already made a better version of this? I want to filter only for my code, see more details (L1 misses), and compare thread loads
110
Pascal @killercup.de · 19/06/2026
I was sick for a week and it made me catch up on sleep as well as on how urgent my work really is. Can’t recommend it tho cause it sucks ro be sick 😅
000
Pascal @killercup.de · 17/06/2026
Waaait what if you add a build dep that hijacks the jobserver pipe and adds random placeholders until ram and cpu are chill? Also for when I need a longer coffee break
110
Pascal @killercup.de · 15/06/2026
Ohh let me know what sharp edges you find, would be a nice fit for github.com/Softleif/bio... because where we're using this, having CUDA is more likely than having Vulkan… and then the CPU fallback is the same
010
Pascal @killercup.de · 09/06/2026
Finally updated my MacBook last weekend so that I can use latest Xcode and also experience this os version for a bit before it gets fixed
010
Pascal @killercup.de · 07/06/2026
Very cool. I’ve been thinking of building an app like instapaper for fun in summer with atproto support. But I was thinking of using the community bookmark lexicon for shares. Why did you decide to go for standard.site instead?
standard.site
Standard.site - One schema. Every platform.
Standard.site provides shared lexicons for long-form publishing on AT Protocol. Making content easier to discover, index, and move across the ATmosphere.
100
Pascal @killercup.de · 20/05/2026
Awesome! Did you post anywhere how you’re hosting eurosky? I’m curious :)
020
Pascal @killercup.de · 15/05/2026
Amos, I have a business idea, but don’t tell anyone: wanna start a company specializing in cleaning up llm rust rewrites? I’m thinking a cute crab in a janitor outfit as a logo. Not sure how long the business model makes sense for tho
040
Pascal @killercup.de · 12/05/2026
Awesome! Yeah it seems you’re doing everything very stream-y :) i basically just put seqair together for my use case so I’m very curious how it fonts in others
000
Pascal @killercup.de · 12/05/2026
Very cool! I recently published deterministic.space/seqair.html which uses a columnar buffer pattern and in my testing was quite a bit faster than noodles (but my use case is a variant caller). Maybe it's useful to you :)
deterministic.space
Seqair, my Rust-native take on htslib
This post introduces seqair , a new Rust library for bioinformatics formats I’ve been working on. We’ll look in detail at one of my main design choices here, a columnar store for iterating BAM data, …
100
Pascal @killercup.de · 09/05/2026
I’ll give this a try when I have time away from algorithm deep dive! You know I’m sucker for cli and config stuff especially based on reflection :)
120
Pascal @killercup.de · 09/05/2026
This is amazing! Way nicer than clap to markdown
120
Pascal @killercup.de · 08/05/2026
Thanks! Yes, didn’t need a reader yet so there is none :)
000
Pascal @killercup.de · 08/05/2026
And second post out as well: bsky.app/profile/dete...
010
Pascal @killercup.de · 08/05/2026
if anyone else cares about this, here's my local caching solution github.com/killercup/sc...
github.com
add caching of kroki diagrams · killercup/scribbles@9005b10
000
Pascal @killercup.de · 08/05/2026
Second post about Seqair, my #rustlang take on htslib. This one is about streaming VCF/BCF writing and type-state/session type APIs! #bioinformatics
130
Pascal @killercup.de · 08/05/2026
mermaid in rust yet?
100
Pascal @killercup.de · 08/05/2026
now on crates.io and especially docs.rs :) docs.rs/seqair/0.1.0... #rustlang #bioinformatics
docs.rs
seqair - Rust
Pure-Rust BAM/SAM/CRAM/FASTA reader, pileup engine, and VCF/BCF writer.
120
Pascal @killercup.de · 08/05/2026
it's super simple to run kroki in docker locally btw, but that only helps me locally, not ci
100
Pascal @killercup.de · 08/05/2026
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
kroki.io
Kroki!
100
Pascal @killercup.de · 04/05/2026
One more #rustlang post! This time on niches for integer ranges using pattern types on nightly!
000
Pascal @killercup.de · 03/05/2026
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
030
Reposted by Pascal
Tangled @tangled.org · 29/04/2026
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.
jobs.tangled.org
Software Engineer, Platform · jobs at tangled
1129559
Pascal @killercup.de · 03/05/2026
Wow, that's fantastic news! I'm in the process of refining the API and fixing some issues I've seen with CRAM performance, before doing a proper 0.1 release. Send me all your feedback :) Feel free to DM me
010