Mastodawn

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

Using Rust typestates for BCF writing

If you’ve ever needed to produce a typed binary format where the header constrains what the body can contain, you’ve probably written validation code that runs at runtime and hoped your tests cover …

Pascal's Scribbles

Pascal 10h ago

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

Using Rust typestates for BCF writing

If you’ve ever needed to produce a typed binary format where the header constrains what the body can contain, you’ve probably written validation code that runs at runtime and hoped your tests cover …

Pascal's Scribbles

Pascal 2d ago

RE: https://hachyderm.io/@Mara/116528385677022441

See you there!

Pascal 4d ago

One more #rustlang post! This time on niches using pattern types on nightly https://deterministic.space/niche-int-types-in-rust.html

Niches for integer types in Rust

While working on seqair (see my post here ), I also wrote a bunch of wrapper types for the domain we work in. One example is Base (a DNA base), which is a fairly straightforward enum. Another is Pos, …

Pascal's Scribbles

Pascal 4d ago

Pascal 6d ago

Spent some time writing about the latest #rust #bioinformatics crate I’ve been working on: seqair, an alternative to (a subset of) htslib with some neat APIs and memory patterns!
If you work in the field: expect a crates.io release soon! If you like software architecture rambles, hope you enjoy the post!
https://deterministic.space/seqair.html

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, …

Pascal's Scribbles

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Pascal 6d ago

If this is of interest to you: what else do you want to read about? I have one or two more posts on this that I want to post :)

Pascal 6d ago

Spent some time writing about the latest #rust #bioinformatics crate I’ve been working on: seqair, an alternative to (a subset of) htslib with some neat APIs and memory patterns!
If you work in the field: expect a crates.io release soon! If you like software architecture rambles, hope you enjoy the post!
https://deterministic.space/seqair.html

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, …

Pascal's Scribbles

Show thread

Pascal Apr 17

Also published a second post on a sub-topic of this, running random forest inference on GPUs: https://deterministic.space/gpu-random-forest-ml.html

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 …

Pascal's Scribbles

Pascal Apr 17

This is what I've been working on for a while now: https://deterministic.space/rastair.html

(Finally got around to blogging again!)

Notes on Rastair, a variant and methylation caller

In the last year, I’ve had the pleasure to work on Rastair , a bioinformatics project by Benjamin Schuster-Böckler from the Ludwig Institute for Cancer Research at the University of Oxford. It is a …

Pascal's Scribbles

Pascal Mar 20

RE: https://genomic.social/@rastair/116260826067877345

Extremely proud to work on this! Challenging and fun

Github	https://github.com/killercup
Blog	https://deterministic.space/
Currently in	Gothenburg 🇸🇪
Pronouns	he/him