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.
right now we have -
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.
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.