Add SN tag (or equivalent) for L lines

[hugocarmaga]

Hi,

Do you think it would be possible (and makes sense) to add the SN tag, or some equivalent new tag, to the L lines of the graph generated by minigraph?

The reasoning here is: when generating a graph, minigraph adds the SN tag to newly introduced nodes, so you can track from which sequence that segment was derived. Additionally to that, in our group we thought it could be useful to also add that information for newly introduced edges, either by just adding the same SN tag or another one specific for that. This would be particularly helpful when trying to track, and even flag/locate, deletion alleles and which sequence introduced them. In our specific case, we start from a pangenome graph, we add a new sample to it, and we want to look at newly introduced variants. We have a way of doing it for insertions, using the SN tags and the BO tags from gaftools. But for deletions, there's no straight forward solution that doesn't involve comparing the two graphs.

We're also aware that the interpretation we want to make out of it might not be generalizable for other cases, but we still think it can be useful. Let us know what you think about it.

Best,
Hugo