canonicalize_modificaitons.identify_ptms assumes modifications are connected components. If this assumption is violated, in combination with the -modify flag, this causes hard to debug user facing errors (see #432 for more background).
This PR resolves that by
1) Log an error for any modification that is not a connected component.
2) Modify the maxwarn mechanism to count all messages >= warning, meaning an error will cause no files to be written. Note that the -maxwarn flag cannot override errors, only warnings.
canonicalize_modificaitons.identify_ptmsassumes modifications are connected components. If this assumption is violated, in combination with the-modifyflag, this causes hard to debug user facing errors (see #432 for more background).This PR resolves that by 1) Log an error for any modification that is not a connected component. 2) Modify the maxwarn mechanism to count all messages >= warning, meaning an error will cause no files to be written. Note that the
-maxwarnflag cannot override errors, only warnings.