Graph distance logic for skipping repetitive anchors in Giraffe doesn't account for the anchor length itself

[adamnovak]

Here we're supposed to be looking at the length of the space between seeds in the graph if we skip a seed.

vg/src/minimizer_mapper_from_chains.cpp

Lines 3035 to 3036 in cbf330b

	if (next_skippable->is_skippable() && next_skippable_it+1 != chain.end() &&
	total_graph_distance+graph_distance < this->max_skipped_bases) {

But we're just summing up the graph distance from the previous anchor to this one, and from this one to the next anchor. We aren't accounting for the length of the anchor itself either for the comparison here, or for the update to total_graph_distance later. So we're systematically underestimating the net distance.

[adamnovak]

@xchang1 Is it meant to be like this for some reason I'm not seeing?

[xchang1]

Yeah, that looks like a bug. I think graph_distance and read_distance should both be including the length of the anchor