Marcus Fedarko

I have an implementation of this ready (for the new version, so not in the SPQR tree but for nodes in the normal graph). All that's left is setting up...

Another idea from Jackie -- if the user uses `-ub`, then output each bubble's composition and corresponding component rank to a human-readable text file. This would be an easier way...

With #182's changes, node searching is in, but it currently lacks searching within patterns. There are some annoying problems that bubble boundary duplication introduces (since now a given node name...

Not really sure how much of this is necessary, though -- the only confusing parts of the application I can think of are the rotation selector and the fit selected...

Update: another approach is adding a "refinement" step, as discussed in Bertault & Miller 1999 (see Fig. 3): https://link.springer.com/content/pdf/10.1007/3-540-46648-7_20.pdf This would remove the similar issue of unnecessary edge crossings. But...

Groups (U or O lines) should be simple to include—U lines (subgraphs) can be encoded as Misc. Patterns in the graph, and O lines (paths) can just be represented as...

Yeah, this would be a useful feature to support. A potential idea for the future is modifying MetaCarvel to output `oriented.gml` as a GFA file, with scaffolds encoded as `O`...

An additional use case for identifying these sorts of patterns: for all the edges located within a bipartite pattern (i.e. between two nodes that are located in the same bipartite...

Coming back to this: a silly property (that I should have thought of earlier) is that these kinds of "cyclic bubbles" (when they are an isolated component of the graph)...

Yeah, doing this (and #61) through Vega-Lite would be much much much easier.