@AngieHinrichs kindly figured out exactly what the bug was here, and what the fix is! It seems to work in the sense that I don't get a crash for the dengue dataset anymore. I have not tested further but am rolling this out because we know the current implementation is wrong. Apologies for the problems and thanks again to Angie for the fix.
v2.0.108 introduced a significant bug in adding support for compound features. This likely means that mutations are misannotated due to not considering previous mutations correctly. It also caused crashes in some circumstances (https://github.com/theosanderson/taxonium/issues/499#issuecomment-1656108278).
@AngieHinrichs kindly figured out exactly what the bug was here, and what the fix is! It seems to work in the sense that I don't get a crash for the dengue dataset anymore. I have not tested further but am rolling this out because we know the current implementation is wrong. Apologies for the problems and thanks again to Angie for the fix.