v2.0.0-beta.2

[nebfield]

Closes #325 #343 #333 #238

See #234

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Changelog

Features

• Add FID support internally (FID + IID must be unique for all samples)
• Add parameters to tune target variant missingness (--pca_geno_miss_target, default maximum 10%) and/or MAF (--pca_maf_target, default no filtering) during intersection with the reference panel.
  • The new defaults will help help incorrect ancestry assignments when running the calculator on low sample sizes (revert to pre-beta version behaviour), as this behaviour was caused by the MAF filter before.
• Add --efo_id parameter, deprecating --trait_efo which will be removed in a future release

Misc

• Remove default anaconda channels because of license changes remove default anaconda channels #342

[smlmbrt]

Looks good to me. I assume we'll wait to merge until we finish the other PRs?

[smlmbrt]

I think we're finished with this release now.