Erik Garrison

I meant to cancel a comment rather than close/reopen. @awz So I'm not wrong in wondering how I could examine the internal structures of the database backing the graph via...

@awz It's expedient to be able to say "there is a node with id=N, get me that node and its context." In vg this is a very core concept: `vg...

@lh3 If this is how things work, then I see a way for me to integrate `vg` with this part of the API. I don't maintain strong identities associated with...

> the very basic graph definition, as based upon Richard's original schema, is very simple, and is an elegant fit to our problem. Exactly. To get pan-genomes up and running,...

> I think you're missing an option (4) in your list, which is to just work in the coordinate space of the original graph, even when looking only at a...

@lh3 asked: > how can we know node 314159 in vg is a reference or a named allele? (In `vg`) we can know if it's a named allele if it...

@lh3 I think there is a misunderstanding. I'm saying that if you have a serialized version of a subset the side graph, you'll want to specify the source offset in...

@richarddurbin observes that > If Erik restricts himself to non-overlapping Reference paths then the models are very similar. It seems there is a conflict here because I would like to...

I guess I am still confused about the design decisions forced by side graphs. If a labeled sequence graph (nodes have sequences/labels, edges are linkages) with named paths is enough...

@benedictpaten What are the benefits of using side graphs as a serialization format? What can we do with a side graph that we can't with a labeled graph where labels...