Henry Davidge

Our BGEN reader always considers the first allele to be the reference. However, the [BGEN spec](https://www.well.ox.ac.uk/~gav/bgen_format/spec/latest.html) does not codify the position of the ref allele, and it can vary from...

We should allow the user to configure these parameters, especially for the approximate Firth fit. cc @bboutkov since I believe this came up in your tests. `logistic_regression` definition: https://github.com/projectglow/glow/blob/master/python/glow/gwas/log_reg.py#L24-L33