--dont_collapse braids a deep nested snarl about gfaffix HOT 3 OPEN

One thing I forgot to mention, is that the original graph is acyclic. gfaffix introduces a cycle when run without --dont_collapse:

for i in *.gfa ; do printf "${i}\t" ; vg paths -x $i -C -Q CHM | awk '{print $3}'; done
chunk_133493101_133529958_fixc.gfa	undirected-cyclic
chunk_133493101_133529958_fix.gfa	undirected-acyclic
chunk_133493101_133529958_raw.gfa	undirected-acyclic

from gfaffix.

1. Braiding structure. Yes, this behavior is inherent to the de-collapse algorithm. I was hoping that removing edges that are not covered by any path would resolve this issue, but apparently, it doesn't.
2. Cycles introduced by de-collapse. I'm not sure this is can be fixed in the current approach.

Both of the issues are non-obvious to fix, they require to refine the de-collapse algorithm. I have to think about it before I can give you a better and definite answer.

from gfaffix.

Sure, thanks!! Any help is appreciated.

from gfaffix.