Makes sense, only minor nits on comments and nomenclature:
 * are you using the words "quality" and "qualityScore" to mean different things? If not, would be good to use just one.

* Might be good to have the header comment state that for matches and mismatches, this is the base quality score. For deletions, it's the mapping quality. For insertions, it's the minimum quality of any base in the insertion. To me, the words "equivalent" and "specific heuristic" are confusing.

* The "in lack of other evidence comments" in the function body are confusing to me. The "heuristic for deletion/insertion" comments I think are unneccessary if the header comment states what's happening for those cases.