pioneer-pi

@jeizenga Exactly, I am executing [Working with a whole genome variation graph](https://github.com/vgteam/vg/wiki/Working-with-a-whole-genome-variation-graph) process. 1. I use ` (seq 1 22; echo X; echo Y) | parallel -j 24 "time vg...

@jeizenga I found another question, when I use `for chr in $(seq 1 22; echo X; echo Y); do vg prune -r $chr.vg > $chr.pruned.vg done` to prune graph, the...

@jeizenga Thanks for you replying. The code `vg paths -L -v 1.pruned.vg ` has no output. I found another thing: I use `vg find -p 1:10000000-10001000 -x 1.xg > sub1.vg`...

@jeizenga That's right! And how to use vg find -c? I can't understand what information need to add after vg find -c and its effect. The vg find help is:...

@jeizenga Thank you very much! And I have a confusion about the length of node sequence. In the subgraph, I found there are many nodes which length is dozens of...

@jeizenga Thank you! https://github.com/vgteam/vg/issues/4206#issue-2074485853 The original question still exists. The following is my operation (I follow the operation of [working with a whole genome variation graph](https://github.com/vgteam/vg/wiki/Working-with-a-whole-genome-variation-graph)): https://github.com/vgteam/vg/issues/4206#issuecomment-1886097522 I did `vg...

@jeizenga I did it and visualized it , found there are new bubbles. So which graph is correct? Why I use `vg find` without `-c `will get a subgraph has...

@jeizenga In addition, I want to know the meaning of snarl file field. For example, the meaning of `type` field in the following line: `{"directed_acyclic_net_graph": true, "end": {"node_id": "1106504"}, "start":...

@jeizenga Now I use vg pack to get a packfile, They are read coverage in each base of variation graph. I want to get all the reads mapping to a...

@glennhickey Thank you