Determines how well-connected a .hal cactus graph file is by measuring how many bases are involved in alignments between each assembly in the graph.
The overall goal of cactus-connectivity is to see which bases in a given assembly/reference aren't aligned to other sequences.
Liftovers help with that by outputting a "target" bedfile that shows the regions in the target sequence that are aligned to the source sequence in positions specified by the source bedfile. In our case, the source bedfile simply includes all positions in the source. Thus, we can find all the regions in the target sequence aligned to the source seq in the graph.
When we want to know the bases that are "free" of alignments in a certain assembly, we want that assembly to be the target. The output of calculate_bases_unmapped will tell us how many bases in the target aren't aligned to the source.