SFS & VCF handling

Site-frequency spectra objects, VCF-to-SFS parsing, ancestral-allele and site-degeneracy annotation, and site filtration are provided by the standalone sfsutils package. fastdfe depends on it and re-exports these classes, so they remain importable directly from fastdfe (e.g. from fastdfe import Spectrum, Spectra, Parser, Annotator, Filterer).

The corresponding sfsutils API reference pages:

• Spectrum classes — the Spectrum and Spectra site-frequency spectra, with folding, polarising, resampling, and visualisation.

• Parsing — the Parser for extracting spectra from VCF files.

• Site stratification — stratifying sites into separate spectra, e.g. by degeneracy or base context.

• Site annotation — the Annotator for ancestral-allele and site-degeneracy / synonymy annotation.

• Site filtration — the Filterer for excluding sites prior to parsing.

• Input and output — reading VCF, FASTA and GFF sources and serialising results.