  Gagie, Navarro and Prezza's $r$-index (SODA, 2018) promises to speed up DNA
alignment and variation calling by allowing us to index entire genomic
databases, provided certain obstacles can be overcome. In this paper we first
strengthen and simplify Policriti and Prezza's Toehold Lemma (DCC '16;
Algorithmica, 2017), which inspired the $r$-index and plays an important role
in its implementation. We then show how to update the $r$-index efficiently
after adding a new genome to the database, which is likely to be vital in
practice. As a by-product of this result, we obtain an online version of
Policriti and Prezza's algorithm for constructing the LZ77 parse from a
run-length compressed Burrows-Wheeler Transform. Our experiments demonstrate
the practicality of all three of these results. Finally, we show how to augment
the $r$-index such that, given a new genome and fast random access to the
database, we can quickly compute the matching statistics and maximal exact
matches of the new genome with respect to the database.
