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pangenome / smoothxg

linearize and simplify variation graphs using blocked partial order alignment
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Fix uncovered edges #194

Closed AndreaGuarracino closed 1 year ago

AndreaGuarracino commented 1 year ago

SPOA and abPOA introduce links not supported by any path, leading to graphs with uncovered edges (see https://github.com/pangenome/pggb/issues/299). This PR avoids that and should fix https://github.com/pangenome/pggb/issues/299. Moreover, it adds a tiny optimization in case there are no blocks to flip.

AndreaGuarracino commented 1 year ago

One nice thing is that the resulting graphs have a bit fewer nodes than before, probably due to better unchop, as we now have fewer links in the graph topology.