More complex 'exclude' allowing a date-check

[emmahodcroft]

Context
Often in ncov (and in other ncov-based builds) we exclude sequences because we believe the dates are wrong. However, once they go into the exclude.txt file, we have to manually remove them if the date is updated. If this is never noticed, it'll stay in exclude forever.

In some other scripts I use for other things, I've created a list that includes both the sequence name (strain) and the sequence date. They are only excluded if both of these match. This means that if the date is updated on GISAID, the sequence is no longer excluded.

Description
An extension to the augur filter function that allows to pass a two-column exclude file - and if a date is present, it is only excluded if the date matches the one given.
Could perhaps also print output showing any that were not excluded as the date didn't match (anymore, presumably). Then users could evaluate if the new date looks good.

This could possibly be an issue in ncov instead, if we wanted to have a script do this work to update the exclude file there - if we think this is a bit more niche to fast-moving data - rather than an augur update. I can move this issue, if so.