decontaminating GTDB itself?

[ctb]

it would be nice to be able to decontaminate GTDB itself, but one of the problems we face there is that charcoal doesn't work well in situations where we have the exact genome in question in the reference database. this is because the first filter is to use gather to search the reference database, and it will return precisely 1 match in that situation.

so the question is, how can we deal with this? two ideas --

• allow the initial gather to be a search, instead, and then tell just_taxonomy.py to ignore exact matches internally.
• find ways to mask or temporarily eliminate specific signatures from the databases.

on GTDB 25k, which is really nice and non-redundant, it should be straightforward (if medium expensive) to do the search, so maybe we should start there.

ref sourmash-bio/sourmash#849

[ctb]

search against GTDB per #122 doesn't seem that bad, perhaps because it's not that redundant.