"Something I think might be useful (at least to me) is the option in collapse duplicates (in pRESTO and/or alakazam) where in the output file the sequence are not actually collapsed but specified annotations are updated accordingly.
This would be useful with complex data sets to identify identical sequences across groups (i.e time points, tissues, isotypes, cell subsets), but maintain their identity in the group."
This is essentially a cloning problem, with a cutoff of zero distance and using the full sequence, so perhaps it's best suited to DefineClones. However, it should be relatively easy to add an option to
collapseDuplicates() that retains the sequences, but combines the annotations, as an immediate solution.