Hierarchical decomposition improvements

[fedarko]

It works pretty well now, but as I've been working with the interface over the past few days I see a few things which should be fixed.

• Disallow frayed ropes from being used in other patterns (including in other frayed ropes): IMO the fact that they have multiple start/end points makes them ambiguous.
  

• If a chain has already been identified and it's a candidate as the start/end node of a bubble, this should be allowed. It isn't currently. Use case: component 75 of the first biofilm graph, contig_0000016197 should form a bubble to contig_0000011283 but since both are in chains this doesn't work.

  • The way to handle this is detecting if the start or end node is a chain, and if so then attempting to "split up" the chain so that its start or end node is now the end or start node of the current bubble. This might be annoying when the chain contains non-basic-node stuff. But basically, we might end up in a situation where splitting the chain completely removes it from the graph, for example if it's just a chain of two nodes...? Hm.

• Allow cyclic chains to be boundary nodes of bubbles (same as with chains).

• Likely related to the above: detect cyclic chains of bubbles. This is a real pattern present in some of the components of the test Velvet E. coli graph, and currently we're detecting 2/3 of the bubbles. Ideally we'd catch all three bubbles and wrap them in a cyclic chain. (What we have now is still, imo, better than what we had previously.)
  Old:
  
  Current:
  
  I am not sure 100% why this is ending up like this; may be a bug in pattern decomp somewhere.

• Probably more things I'm not thinking of / haven't run into yet

Honestly, this already looks pretty nice, so these fixes are low priority since they're pretty subjective

[fedarko]

Oh, for reference, the bug with cyclic chains and bubbles was due to the end "node" (bubble) pointing to the start "node" (also a bubble), preventing bubbles from being created. for the time being i allowed bubbles to be formatted like this, which results in cyclic chains of at least 3 bubbles being ok. (Still gotta make this work for 2-bubble cycles, which are a bit trickier... see #167)

[fedarko]

Splitting up into multiple issues; closing.