In the 0.22.0 version, I updated the api.utils.estimate_phase_beagle() method to resolve a minor bug where Beagle’s expectation-maximization algorithm estimated a parameter value that was outside the permitted range (see 29a7d6f, #113, and also the CHANGELOG).
However, during this update, I inadvertently overlooked renaming the variable vf to vf3:
The oversight carries significant implications, particularly if the user's input VCF contains sample names that overlap with the reference panel or if there are differences in chromosome annotation compared to the reference panel (e.g. chr22 vs. 22).
In the 0.22.0 version, I updated the
api.utils.estimate_phase_beagle()method to resolve a minor bug where Beagle’s expectation-maximization algorithm estimated a parameter value that was outside the permitted range (see 29a7d6f, #113, and also the CHANGELOG).However, during this update, I inadvertently overlooked renaming the variable
vftovf3:https://github.com/sbslee/pypgx/blob/f6ad1d30241e217e77b0dc4f0a7045bc8cf9cf47/pypgx/api/utils.py#L859-L864
The oversight carries significant implications, particularly if the user's input VCF contains sample names that overlap with the reference panel or if there are differences in chromosome annotation compared to the reference panel (e.g.
chr22vs.22).