gfatools bubble doesn't work on GFA after bubble popping with gfatools asm

[lstevens17]

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