Option to consider last allele as reference in BGEN reader

[henrydavidge]

Our BGEN reader always considers the first allele to be the reference. However, the BGEN spec does not codify the position of the ref allele, and it can vary from dataset to dataset.

We should accept a datasource option to configure this behavior. Relevant code: https://github.com/projectglow/glow/blob/master/core/src/main/scala/io/projectglow/bgen/BgenFileIterator.scala#L97

[ptn24]

Alternatively, it could be good to support aligning with a particular reference genome after the fact. More of an "ELT" approach