Hi @glennhickey, I had a question about rgfa tags, specifically the stable sequence rank. My understanding from the rgfa-split code is that a node rank i must be connected to a node rank i - 1, if i > 0. I don't quite understand how this works in practice. In a simple graph with 5 nodes, one source, one sink, and 3 "alt allele" nodes that form three paths from source to sink, we can label the first node rank 0 (the reference path), and the others rank 1 and 2. But in this case, the rank 2 node is not connected to a rank 1 node, only rank 0 on both sides. How is this dealt with? Or am I misunderstanding how ranks work?
Also, what should happen if two sequences have the same alt allele path through a bubble with one node per path? Which sequence's rank should be assigned to the node? both? or the lowest rank?
Thanks for the clarifications!
Hi @glennhickey, I had a question about rgfa tags, specifically the stable sequence rank. My understanding from the
rgfa-splitcode is that a node rank i must be connected to a node rank i - 1, if i > 0. I don't quite understand how this works in practice. In a simple graph with 5 nodes, one source, one sink, and 3 "alt allele" nodes that form three paths from source to sink, we can label the first node rank 0 (the reference path), and the others rank 1 and 2. But in this case, the rank 2 node is not connected to a rank 1 node, only rank 0 on both sides. How is this dealt with? Or am I misunderstanding how ranks work?Also, what should happen if two sequences have the same alt allele path through a bubble with one node per path? Which sequence's rank should be assigned to the node? both? or the lowest rank?
Thanks for the clarifications!