--- title: "Seqair, my Rust-native take on htslib" url: https://daily.dev/posts/seqair-my-rust-native-take-on-htslib-9puntghme source_url: https://deterministic.space/seqair.html type: article source: "Pascal’s scribbles" published: 2026-04-30T18:36:11.962Z updated: 2026-04-30T18:36:34.657Z tags: ["rust", "biotech"] reading_time: 17 upvotes: 0 comments: 0 language: en --- > ## Documentation Index > Fetch the complete documentation index at: https://daily.dev/llms.txt > Use this file to discover all available pages before exploring further. # Seqair, my Rust-native take on htslib **[Pascal’s scribbles](https://daily.dev/sources/deterministicspace)** · 17 min read · 0 upvotes · 0 comments ## Summary Seqair is a new Rust-native library for bioinformatics file formats (SAM/BAM/CRAM/VCF/BCF), built as an alternative to htslib and rust-htslib. The core design innovation is a columnar record store for BAM data: instead of per-record heap allocations, variable-length fields (names, bases, CIGAR, quality, aux tags) are stored in contiguous slabs with offsets, enabling near-zero allocations in the hot loop and efficient in-place realignment by appending new CIGAR data. Other highlights include a type-state builder API for VCF/BCF writing, a forkable reader design using Arc for shared immutable state across rayon worker threads, and a RegionBuf that merges BAM index chunks into minimal large reads to reduce NFS round-trips on HPC clusters. Benchmarks show seqair is competitive with htslib on pileup and BCF writing, with a notable 2.5x win on BCF. The CRAM implementation was largely generated by Claude Code from the spec and is acknowledged as not production-ready. ## Full article daily.dev links to this article rather than hosting it. Read it at the original source: ## Similar posts on daily.dev - [Notes on Rastair, a variant and methylation caller](https://daily.dev/posts/notes-on-rastair-a-variant-and-methylation-caller-ponbubbko) · Pascal’s scribbles · 1 upvotes · 0 comments - [Using Rust typestates for BCF writing](https://daily.dev/posts/using-rust-typestates-for-bcf-writing-jnagdofxn) · Pascal’s scribbles · 0 upvotes · 0 comments - [Let's see Paul Allen's SIMD CSV parser](https://daily.dev/posts/let-s-see-paul-allen-s-simd-csv-parser-xr1qamezs) · Lobsters · 0 upvotes · 0 comments - [zlib-rs 0.6.4 Released With Fix For Intel Raptor Lake Crash, SIMD Optimizations](https://daily.dev/posts/zlib-rs-0-6-4-released-with-fix-for-intel-raptor-lake-crash-simd-optimizations-sddc5t54e) · Phoronix · 0 upvotes · 0 comments --- Tags: [#rust](https://daily.dev/tags/rust), [#biotech](https://daily.dev/tags/biotech) [View this post on daily.dev](https://daily.dev/posts/seqair-my-rust-native-take-on-htslib-9puntghme)