I built a pangenome using the minigraph-cactus pipeline, and converted the .gbz to a gfa for building in odgi, e.g.
vg convert -x Pgcactus.gbz -f --vg-algorithm > ../Pgcactus.gfa
If I run vg paths -x Pgcactus.gfa I can confirm that the reference paths are in the graph,
However, after I run:
odgi build -g Pgcactus.gfa -o Pg_unsorted.og
followed by:
odgi paths -i Pg_unsorted.og -L
the reference paths are no longer listed -- this is a problem because I want to be able to run odgi position to get the nearest reference node, as in the tutorial, e.g. odgi position -i k.og -g 4 -r x
Is this a bug, or am I doing something wrong? I would greatly appreciate any suggestions.
Hello,
I built a pangenome using the minigraph-cactus pipeline, and converted the .gbz to a gfa for building in odgi, e.g.
vg convert -x Pgcactus.gbz -f --vg-algorithm > ../Pgcactus.gfaIf I run
vg paths -x Pgcactus.gfaI can confirm that the reference paths are in the graph,However, after I run:
odgi build -g Pgcactus.gfa -o Pg_unsorted.ogfollowed by:
odgi paths -i Pg_unsorted.og -Lthe reference paths are no longer listed -- this is a problem because I want to be able to run odgi position to get the nearest reference node, as in the tutorial, e.g.
odgi position -i k.og -g 4 -r xIs this a bug, or am I doing something wrong? I would greatly appreciate any suggestions.