breaking paths and using extents to maintain contiguity

[ekg]

An important operation is to remove nodes from the graph. For instance, we might want to remove low-coverage nodes.

This can cause us to remove nodes in the middle of paths, breaking them. We have no way to represent this, and so I think most of our implementations will just remove the entire path.

@adamnovak had the idea of an "extent", where we know how much sequence was lost, but we don't represent the sequence. This is a great idea, but we have no way to serialize it in GFA. So, let's clarify exactly the semantics we want, present it to the GFA spec group, and implement this in all of the path handle graph libraries.