Post

Pascal
@killercup.de

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

deterministic.spaceSeqair, my Rust-native take on htslibThis 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, …

2 reposts10 likes

Benjamin Schuster-Böckler
@dagams.bsky.social

💯 htslib is so fundamental to so many NGS applications. Having an equivalent API but with a cleaner backing is exactly what we need to accelerate development in this space. Thanks again for putting that work in, really great to see how work on rastair has positive impact far beyond its scope

Seth Stadick
@ducktapeprogrammer.bsky.social

Awesome write up, thanks for sharing it! Love the slab idea. I’ll have to try it out in perbase as that’s the exact access pattern that should speed it up a bit. How did using Tracey go for you? Was kt worth the effort?

Pascal
@killercup.de

Let me know if you try it! Tracey has been pretty nice to work with but I’ve mainly used it to write some basic specs myself and then to keep claude in check 😄 I’m sure I overdid it even and it’s too specific now!

Pascal
@killercup.de

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