Verify ref / alt orientation correctness for files incorporated in v2

[mikegloudemans]

For those present in the code base before 2019, I did my best to get the effect polarity correct, although there may still be some errors

For all files included only in the v2 (Spring 2020) update, I got the polarity correct if it was clear from the header titles, but didn't do any double-checking to verify that the "effect" allele is truly the one to which the effect column beta or OR applies

[mikegloudemans]

Come up with a system for marking confidence level in the correctness of these. It's not always clear which is effect allele vs. non-effect allele unless that specific terminology is used