Make it possible to set a coverage and/or identity threshold that only covers proteins.faa when using --proteins

[avonm]

Hi,

Not sure if this is possible... It would be nice when using the --proteins option to set a specific coverage/identity threshold for just those proteins and at the same time keep the default coverage threshold (80) for the rest of the annotations. This would make it possible to add annotations from a list of proteins, e.g. specific virulence genes (that are often not annotated correctly). Or maybe it's possible to annotate a second time against my own protein database and then choose a different coverage threshold?

Best, Astrid