Valid paths in a GFA don't have end-to-end alignments

[rlorigro]

Hi,

I am cross-posting this issue which I have submitted to the PanAligner repository, since it has been found by the authors to be a result of the base-level alignment step taken from minigraph/gwfa.

In summary, if I take a simple 3 node graph in which the middle node could be viewed as an insertion, and I concatenate the three nodes as a query, minigraph fails to find an end-to-end alignment. The shortest node is 38bp.

Thanks

PS: to clarify I've run the exact same test with minigraph and found the same results