remove -V since I'm trying to get rid of the option

[faithokamoto]

I think this is why vgteam/vg#4846 was failing tests.

[adamnovak]

@faithokamoto Don't you have to get rid of the vg combine calls at https://github.com/vgteam/toil-vg/pull/865/changes#diff-eadbbfbb1c9df2f9c4dbc62195ee9c713aff8008d14812ab03f68fadf5c3ef16R1583-R1588 and https://github.com/vgteam/toil-vg/pull/865/changes#diff-eadbbfbb1c9df2f9c4dbc62195ee9c713aff8008d14812ab03f68fadf5c3ef16R1755-R1758 ?

It looks like now instead of taking a graph file with just the path(s) and no nodes, and combining it into a base graph, you're taking a graph file with the path and all the nodes, and combining it into the base graph that also has the nodes. Since vg combine says it will re-number nodes in the graphs being combined to avoid conflicts, it sounds like you're going to end up with graphs files with two whole copies of the graph in them, one of which has the path(s).

I think you want to drop the vg combine and just have vg paths --retain-paths write directly to the file that vg combine was going to write.