multi-stage charcoal?

[ctb]

right now we have -

• stage 1 - hit list
• stage 2 - clean based on hit list.

with the idea that the hit list is something you edit, and then run clean.

however, with the advent of reporting, I'm starting to think we want a more explicit three stage.

• stage 1 - generate initial contamination report, and produce a hit list for user to inspect/edit. here, the user would provide lineages for genomes without lineage ident, and otherwise tune the basic configuration.
• stage 2 - based on first round hit list, produce a summary report of what has been removed, what is left; encourage user to edit, tune, etc.
• stage 3 - do final cleaning

the only problem here is that stage 2 would probably involve some kind of interactive configuration where the user would select taxonomic lineages to keep or drop.

I dunno, sounds complicated from a UX experience. sigh... maybe I'll leave it for future versions.