ksamuk/pixy

AI Summary: A user updated `pixy` from beta 8 to beta 12 and observed a significant reduction in the reported number of SNPs (`no_snps`) in the Fst output, even when processing a biallelic VCF without using the new multiallelic SNP parameter. This indicates a potential regression or an undocumented change in SNP counting or filtering logic between the two beta versions, leading to different results for identical inputs.

AI Summary: The user is attempting to run `pixy` v2.0 on a VCF containing mixed-ploidy individuals (haploid males, diploid females) on the X chromosome. `pixy` infers a single ploidy and advises splitting the VCF, leading the user to question if it's possible to analyze such data in a single run or if separate analyses for each ploidy group are required. The issue seeks clarification on `pixy`'s current capabilities regarding variable ploidy within a single chromosome analysis.

AI Summary: A user encountered a `ModuleNotFoundError` for `typing_extensions` when installing `pixy 2.0.0.beta12` on Python 3.11. This indicates that `typing_extensions` is a missing dependency for the `pixy` package. The suggested fix is to add `typing-extensions` to the project's requirements.