Pascal
@killercup.de
📤 81
📥 119
📝 111
Freelance Rust nerd Blog:
@deterministic.space
Pronouns: He/him Location: Sweden
Second post about Seqair, my
#rustlang
take on htslib. This one is about streaming VCF/BCF writing and type-state/session type APIs!
#bioinformatics
add a skeleton here at some point
8 days ago
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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
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Kroki!
https://kroki.io/
8 days ago
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One more
#rustlang
post! This time on niches for integer ranges using pattern types on nightly!
add a skeleton here at some point
12 days ago
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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
add a skeleton here at some point
13 days ago
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Pascal
Tangled
17 days ago
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.
add a skeleton here at some point
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reposted by
Pascal
Pascal’s scribbles blog
17 days ago
Seqair, my Rust-native take on htslib
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Seqair, my Rust-native take on htslib
https://deterministic.space/seqair.html
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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
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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, …
https://deterministic.space/seqair.html
16 days ago
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I was about to write a blog post after having done some research here but I see everyone already published that post today
add a skeleton here at some point
17 days ago
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reposted by
Pascal
Pascal’s scribbles blog
24 days ago
Still blogging
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Still blogging
https://deterministic.space/still-blogging.html
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The best kind of blog posts about blog tooling and blog redesigning, right?
add a skeleton here at some point
23 days ago
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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?
24 days ago
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Wow,
kroki.io
is pretty awesome to include diagrams as svg in hugo! and with enough `!important`, it even works well with dark mode
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Kroki!
https://kroki.io/
26 days ago
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reposted by
Pascal
Pascal’s scribbles blog
29 days ago
Random Forest ML on GPU
deterministic.space/gpu-random-f...
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Random Forest ML on GPU
In my recent post on Rastair , we looked at some performance best-practices and optimizations for Rastair , a bioinformatics tool that I’m currently working on. One of the slowest parts of the tool is...
https://deterministic.space/gpu-random-forest-ml.html
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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.
29 days ago
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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?
about 1 month ago
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reposted by
Pascal
Pascal’s scribbles blog
about 1 month ago
Using CSS vars to style SVG symbols
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Using CSS vars to style SVG symbols
https://deterministic.space//css-in-svg-symbols.html
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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
about 1 month ago
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reposted by
Pascal
Pascal’s scribbles blog
about 1 month ago
Notes on Rastair, a variant and methylation caller
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Notes on Rastair, a variant and methylation caller
https://deterministic.space//rastair.html
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Finally wrote a post about the project I’ve been working on! And gave my blog an account
add a skeleton here at some point
about 1 month ago
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Not sure this is on purpose but I just found a new business model for myself
add a skeleton here at some point
about 1 month ago
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Pascal
Rust Language
about 1 month ago
⚠️ 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.) ⚠️
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Finally, I'm writing file readers and have an excuse to use fuzzers again!
about 1 month ago
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Pascal
bioRxiv Bioinfo
about 2 months ago
Rastair: an integrated variant and methylation caller
https://www.biorxiv.org/content/10.64898/2026.03.19.712983v1
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Pascal
Benjamin Schuster-Böckler
about 2 months ago
🎉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 🔥
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https://www.biorxiv.org/content/10.64898/2026.03.19.712983v1
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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?
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GitHub - Softleif/cstr8: string types that are both valid UTF-8 and nul-terminated
string types that are both valid UTF-8 and nul-terminated - Softleif/cstr8
https://github.com/Softleif/cstr8
about 2 months ago
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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
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Introduction - Rastair
Rastair is a command-line tool to process epigentic sequencing data. It can call genetic variants and DNA methylation simultaneously from Illumina™ 5base and TAPS+.
https://www.rastair.com/
about 2 months ago
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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 😅
about 2 months ago
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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!
2 months ago
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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
2 months ago
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Is it weird that I as a human have more fun reading skill files compared to actual programming books?
add a skeleton here at some point
3 months ago
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@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 :)
3 months ago
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Pascal
Year Progress Bot
5 months ago
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Pascal
FerrousSystems
5 months ago
🦀 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...
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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
6 months ago
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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!
6 months ago
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Pascal
The Rust Foundation
6 months ago
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 🦀
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Launching the 2025 State of Rust Survey | Rust Blog
Empowering everyone to build reliable and efficient software.
https://blog.rust-lang.org/2025/11/17/launching-the-2025-state-of-rust-survey/
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Pascal
Adam Leventhal
6 months ago
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"
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Oxide and Friends 11/3/2025 -- Futurelock
YouTube video by Oxide Computer Company
https://www.youtube.com/watch?v=cqpLGvalyrI
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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?
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https://quoteinvestigator.com/2016/12/30/not-malice/
7 months ago
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There are only a few projects whose release notes excite me and
@typst.app
is one of them
add a skeleton here at some point
7 months ago
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What's this pattern in
#rustlang
called, where you use a block to initialize a variable? I use it all the time
7 months ago
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Pascal
Benjamin Schuster-Böckler
7 months ago
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!
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Pascal
Pascal
7 months ago
At
#EuroRust
and picking the talks about stuff I would never look into otherwise :) cosmic was interesting and now learning about Petri nets
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Pascal
Pascal
7 months ago
Going to
@eurorust
this week! Been a while since I’ve been to a rust conference, looking forward to it :)
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Pascal
Pascal
10 months ago
Wrote a blog post about this, I thought it was quite interesting
https://deterministic.space/bufwriter-lz4.html
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Rust BufWriter and LZ4 Compression
Recently, I’ve been working on a Rust project again.It deals with bioinformatics data, which can be quite large,so I got to play with profiling and optimizing the code.I’ve done some of this in past, but this time it was actually useful.In this post, I want to talk about a small optimizationin working with LZ4 compressionthat made a big difference in runtime performance.
https://deterministic.space/bufwriter-lz4.html
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I wrote a blog post about fiddling with buffered LZ4 writers in
#rustlang
deterministic.space/bufwriter-lz...
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Rust BufWriter and LZ4 Compression
Recently, I’ve been working on a Rust project again.It deals with bioinformatics data, which can be quite large,so I got to play with profiling and optimizing the code.I’ve done some of this in past, ...
https://deterministic.space/bufwriter-lz4.html
10 months ago
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Pascal
Pascal
11 months ago
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
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Pascal
Pascal
11 months ago
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
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Pascal
Benjamin Schuster-Böckler
11 months ago
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.
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Job Details
https://cutt.cx/bsky1
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That looks like a really cool job! I’ll be looking for contracting jobs from September again, but this is tempting!
add a skeleton here at some point
about 1 year ago
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