First stable release of sfsutils, consolidating extensive correctness, performance and robustness work on the beta.
Input sources. Parse from VCF files, VCF-Zarr stores and tskit tree sequences (ARGs) interchangeably through a single source argument.
Spectra. Derive the one-dimensional SFS, the joint (multi-population) SFS, and the two-site SFS (2-SFS), each with its own folding, covariance and plotting support.
Command line. A sfsutils command-line tool with parse, filter and annotate subcommands.
Performance. Significant speedup across parsing and annotation, with indexed coding-sequence and FASTA lookups so annotation no longer scales with the annotation file.
Memory. The VCF-Zarr writer streams to the store in chunks, keeping its footprint flat regardless of the number of sites.
Correctness. Numerous fixes to the numbers produced, including the two-site SFS extrapolation, joint SFS folding, and consistency across the VCF, VCF-Zarr and tree-sequence backends.
Compatibility. Requires Python 3.11 or newer.
Install with pip install "sfsutils-popgen[vcf,zarr,arg]". See the documentation for all the details.