seqair

Pure-Rust BAM/SAM/CRAM/FASTA reader with a pileup engine. I/O backend for rastair.

This repo has two crates:

• seqair: Indexed readers and pileup engine
• seqair-types: Core types: Base, Strand, Phred, Probability, RegionString

Highlights

• Spec-driven development using tracey
• Slab-based RecordStore — zero per-record heap allocation
• RegionBuf bulk I/O — one large read per region, then decompress from memory (good for NFS/Lustre)
• CRAM v3.0/v3.1 (rANS, tok3, bzip2, lzma, multi-ref slices, embedded refs, MD5 verification)
• Overlapping read-pair dedup built into the pileup engine
• fork() for cheap per-thread readers sharing index and header via Arc
• ChunkCache for distant BAI bins — loads wide-spanning chunks once per chromosome

Testing

cargo test

Comparison tests in crates/seqair/tests/ validate against rust-htslib (and sometimes noodles). Property tests use proptest.