Hello,
I'm having trouble running gfatools bubble
on a GFA file that has been processed with with gfatools asm
.
I'm working with a subgraph that I extracted from minigraph
output using gfatools view
. If I run gfatools bubble
on this subgraph file, I get the expected BED file:
$ gfatools bubble test_subgraph.gfa | head -n 1
V 19985854 19985854 2 1 0 0 0 -1 -1 -1 s54242,s54243 * *
And everything looks as expected in bandage.
However, if I then pop bubbles in this graph using gfatools asm
(command: gfatools asm -b 10000 -u test_subgraph.gfa >test_subgraph.b10000u.gfa
), and then try to run gfatools bubble
on the output, I get nothing:
$ gfatools bubble test_subgraph.b10000u.gfa | head -n 1
This GFA looks as expected in bandage (same structure as before, but fewer segments/bubbles), and I can generate a FASTA using gfatools gfa2fa
. However, in addition to gfatools bubble
not working, gfatools gfa2bed
also produces nothing.
Is there anyway to get this second file to work with gfatools bubble
? Is this something to do with GFA vs rGFA?
Thanks for your help!
I've attached the example files as .txt as github wouldn't accept my GFA files:
test_subgraph.b10000u.gfa.txt
test_subgraph.gfa.txt
And I'm using the following version of gfatools:
$ gfatools version
gfa.h: 0.5-r244-dirty
gfatools: 0.5-r238-dirty