Self-loop and cycles in rGFA

[gsc74]

@lh3 In rGFA file (test\MT.gfa) there is a self loop, So can we expect graph generated with minigraph -cxggs or minigraph --ggen to contain self-loops or cycles?

[lh3]

The example just shows that minigraph can handle cycles. I don't think the current minigraph can generate cycles (I haven't checked), but it can generate inversions, which may be more difficult to handle downstream.

[gsc74]

Thanks!

[gsc74]

@lh3 I've checked hprc-v1.0-minigraph-chm13.gfa graph from hprc, by converting to vg format;

vg convert -gv hprc-v1.0-minigraph-chm13.gfa -t 128 > hprc-v1.0-vg-chm13.vg

followed by;

vg stats -A hprc-v1.0-vg-chm13.vg

It shows graph is cyclic

[glennhickey]

Note: vg stats -A checks for both "reversing" and "non-reversing" cycles, ie if you can start at some node, walk on the graph, and get back to your starting node in either orientation, it will report "cyclic". This also means that a single inversion would be enough to have your graph considered cyclic by this tool.

[gsc74]

Thanks!