gfaffix invalidates graph by removing self-looping edge

[glennhickey]

This issue comes courtesy of ComparativeGenomicsToolkit/cactus#1123

Note that to reproduce, you need a vg version < 1.50.0 due to this issue!

gfaffix --version
gfaffix 0.1.4b

vg version
vg version v1.49.0 "Peschici"

wget -q http://public.gi.ucsc.edu/~hickey/debug/gfaffix-crash-aug4-2023/NW_017567117.1.vg.gfa.gz
gzip -d NW_017567117.1.vg.gfa.gz

vg validate NW_017567117.1.vg.gfa
graph: valid

gfaffix NW_017567117.1.vg.gfa --output_refined NW_017567117.1.vg.gfaffixed.gfa --check_transformation --dont_collapse GCF_0016612551* > /dev/null

vg validate NW_017567117.1.vg.gfaffixed.gfa
graph invalid: missing edge between 691th step (86210:1) and 692th step (86210:0) of path GCA_0193217651#0#JAHTLY010002216.1#0
graph invalid: missing edge between 692th step (86210:1) and 691th step (86210:1) of path GCA_0193217651#0#JAHTLY010002216.1#0
graph: invalid

[danydoerr]

Ouch. Thanks for reporting! I'll try to fix this as soon as possible.

[mjhubisz]

Hi,
I stumbled onto this after getting an error very much like ComparativeGenomicsToolkit/cactus#1123, but we are using newest release of cactus (via docker). I am still getting the same results as glenn posted here, can you check?

root@c0cdf4b8c2e2:/data# gfaffix --version
gfaffix 0.1.5
root@c0cdf4b8c2e2:/data# vg version
vg version v1.51.0 "Quellenhof"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux
Linked against libstd++ 20230528
Built by anovak@courtyard.gi.ucsc.edu

root@c0cdf4b8c2e2:/data# wget -q http://public.gi.ucsc.edu/~hickey/debug/gfaffix-crash-aug4-2023/NW_017567117.1.vg.gfa.gz^C
root@c0cdf4b8c2e2:/data# gzip -d NW_017567117.1.vg.gfa.gz
root@c0cdf4b8c2e2:/data# vg validate NW_017567117.1.vg.gfa
graph: valid
root@c0cdf4b8c2e2:/data# gfaffix NW_017567117.1.vg.gfa --output_refined NW_017567117.1.vg.gfaffixed.gfa --check_transformation --dont_collapse GCF_0016612551* > /dev/null
root@c0cdf4b8c2e2:/data# vg validate NW_017567117.1.vg.gfaffixed.gfa
graph invalid: missing edge between 691th step (86210:1) and 692th step (86210:0) of path GCA_0193217651#0#JAHTLY010002216.1#0
graph invalid: missing edge between 692th step (86210:1) and 691th step (86210:1) of path GCA_0193217651#0#JAHTLY010002216.1#0
graph: invalid

[danydoerr]

@mjhubisz Thanks for the report & the data. I'll have a look early next week.

[danydoerr]

@mjhubisz Turns out the fix was reversed by subsequent commit a0395b5 and thus didn't made it into the release. It's a shame that this remained unnoticed for so long. Current main on git should work now, I'll push a release soon.

[mjhubisz]

Thanks so much!