gfaffix invalidates graph by removing self-looping edge #11
Description
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