We have occasionally encountered sequence variants that simultaneously disrupt a footprint and create a different one (judged by footprint shape).
Our "total.damage" score is cumulatively summing up the damage scores over all k-mer pairs of a variant and so occasionally fails
to flag up such variants. To address this shortcoming, we have introduced the "total.absolute.damage" score which sums up the absolute values of
the k-mer comparisons over a variant. While this score is subject to more noise (opposite small changes don't cancel each other out anymore), it is capable
of highlighting complex footprint changes worth investigating.
We recommend a total.absolute.damage score of 1.0 as rule of thumb threshold. And always check the footprint profiles. Happy Footprinting!