GFAffix breaks path

[glennhickey]

I've run into a rare problem with gfaffix where it seems to leave an invalid path on this graph. Here is how to reproduce:

wget http://public.gi.ucsc.edu/~hickey/debug/chr2.vg.gfa.gz
gzip -d chr2.vg.gfa.gz
gfaffix chr2.vg.gfa --output_refined chr2.gfaffixed.gfa --dont_collapse "GRCh38*" 2> gfaffix.stderr > gfaffix.stdout
vg validate chr2.gfaffixed.gfa
graph invalid: missing edge between 67753th step (7866944:0) and 67754th step (7861328:0) of path HG03579.1.JAGYVU010000149.1
graph invalid: missing edge between 67754th step (7861328:1) and 67753th step (7866944:0) of path HG03579.1.JAGYVU010000149.1
graph: invalid

[glennhickey]

Here's a more manageable example

wget -q http://public.gi.ucsc.edu/~hickey/debug/chr14.gfa.gz
gzip -d chr14.gfa.gz
vg validate chr14.gfa
graph: valid
gfaffix chr14.gfa --output_refined chr14.gfaffix.gfa --dont_collapse "GRCh38*" > /dev/null
vg validate chr14.gfaffix.gfa
graph invalid: missing edge between 547163th step (2438295:0) and 547164th step (2433572:0) of path HG00673.1.JAHBBZ010000004.1
graph invalid: missing edge between 547164th step (2433572:1) and 547163th step (2438295:0) of path HG00673.1.JAHBBZ010000004.1
graph: invalid

Interestingly, this happens in the presence of a huge node:

grep ^S chr14.gfaffix.gfa | grep 2438295 | wc
831317

Chopping the graph seems to help:

vg mod -X 1000 chr14.gfa > chr14.chop.gfa
gfaffix chr14.chop.gfa --output_refined chr14.chop.gfaffix.gfa --dont_collapse "GRCh38*" > /dev/null
vg validate chr14.chop.gfaffix.gfa
graph: valid