Refactoring of the code and the taking in of comments received from active users:
Fixed several edge cases and inconsistencies in the coloring of data from Ultima Genomics.
Refactored indel coloring code for clarity.
Added a new option to the Alignment display preferences "INDEL coloring uses min quality (ultima)" that colors indels by the minimal quality of the homopolymer run rather than by the quality of the specific change.
Thanks to Thomas Garrety (Hartwig Foundation) for insightful comments and feature suggestions.
Refactoring of the code and the taking in of comments received from active users: