Documenting gaps in AGP scaffolds

[fedarko]

Ambitious extension of #205.

The idea is that AGP files can describe gaps in a scaffold. If such a gap occurs between two adjacent contigs in a scaffold, and these contigs are adjacent to each other in the graph, it might be nice to indicate this gap's presence somehow. Maybe by adding a special symbol that shows up on the edge connecting these contigs?

The obvious question is how do we handle this when the contigs flanking the gap are not adjacent, and the answer to that question is a resounding "idk". Something worth documenting, anyway.

See also: "jump" (GFA1) / "gap" (GFA2) edges (#147).