Depth implementation

[sampsyo]

Great. If that's really how simple the depth algorithm is in its most basic form, then I guess that's good news.

I have two suggestions related to things to keep in the repository, which will be useful for our long-term sanity:

• Let's not include "intermediate" files. In this case, this means .og files that we generate from .gfa files. The "source of truth" is in the original .gfa file, and the .og file is derived, so keeping it around is (a) redundant and (b) error-prone if it gets out of date. (This is analogous to the advice never to check in .o files that are the result of compiling C programs.) Instead, let's include some sort of recipe for generating these files. Maybe a Makefile or even just a README saying how to create them.
• This is a less hard-and-fast rule, but let's mostly avoid checking in "other people's data." In this case, that means the .gfa files. They are available elsewhere on the Internet, so no need to include them in our repository. Instead, as with the previous bullet point, we can just provide a recipe (either machine-executable or human-readable) for obtaining them.

I'll try to briefly show y'all what I mean in an upcoming PR…

[sampsyo]

(BTW, including the extremely tiny k.gfa file is probably an exception to the second item, because it is so incredibly tiny…)