Explore conflicts at species and genus level.
- thapbi_pict.conflicts.main(db_url: str, output_filename: str, debug: bool = False) int
Looks for taxonomy conflicts at marker, genus or species level, with the number of marker or genus level conflicts used as the return code. i.e. Unix failure (non-zero) when there are marker or genus level conflicts.
A marker level conflict is when a unique sequence appears in the DB under more than one marker name (e.g. both COI and ITS1), which is most likely an error in the DB construction.
Genus level conflicts are where a unique sequence in the DB is reported from more than one genus, which is considered undesirable. Similarly for species level conflicts, but for some markers this is sadly common and not considered to be an error.