Open AndreaGuarracino opened 3 years ago
I'd suggest 2 things:
-c
to pull in nodes adjacent to your path. it defaults to 0 in vg find which probably won't give what you wantvg chunk
instead of vg find
. (the relevant options remain the same). vg chunk
is more careful to not make path fragments that will cause trouble downstreamThank you @glennhickey! Using -c
with vg find
didn't work, but using vg chunk
plus -c
I was able to get the graph's chunk.
Does it mean that vg find
is going to be deprecated?
1. What were you trying to do? I was trying to extract a subregion from a graph encoded in a GFA format file.
2. What did you want to happen? I want to obtain a GFA format file with the graph subregion plus the paths' portions covering that subregion.
3. What actually happened? I get this error
error[load_proto_to_graph]: duplicate rank 5944 in path hg38_chr2
4. If you got a line like
Stack trace path: /somewhere/on/your/computer/stacktrace.txt
, please copy-paste the contents of that file here: -5. What data and command can the vg dev team use to make the problem happen?
Here the input used.
6. What does running
vg version
say? vg: variation graph tool, version v1.30.0 "Carentino"