Make vg combine handle subpaths and link chunked graphs (for chunked augmentation) #2688

I would like to be able to chunk a graph, modify the chunks (e.g augmenting with variants in the "middle" of the chunk) and combine them back together.

I think vg combine works with disjoined chunks (different chromosomes) but when I try it on chunks that share a path, e.g. a chromosome split in multiple chunks, it complains about "duplicated rank 1 in path ..." and wouldn't link the chunks together anyway (AFAIK).

Assuming that I was careful and the tails of my chunks are unchanged by whatever I'm doing to the chunks, could it be possible to combine chunks and have vg combine:

• stitch the "duplicated" subpaths if they spanned multiple chunks, back into the reference path for example.
• have the chunks linked, i.e. adding an edge from the end or the previous chunk to the beginning of the next one, or something of the like.

What do you think? Am I missing something?

I would have to combine each chromosome separately and make sure the new nodes created when working on a chunk don't conflict with other chunks. I think vg ids -j would handle that.