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 22h 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

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Pascal 1d ago

@yosh !!!11

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 5d ago

Pascal May 2

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, …

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Pascal 6d ago

@kloetzl nice! would love to collab if the designs overlap :) i'm trying to support all the edge cases i find but optimize for the usual case when possible

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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 :)

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Pascal May 2

@amanjeev Thank you! <3 It's great fun and a very deep rabbit hole! You're more than welcome to check out the code and point out some mistakes, I assume there are many :)

Pascal May 2

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

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