Some snarls are missed after normalizing the input vg file

[daanishmahajan]

Hi @ekg

1. What were you trying to do?
I am trying to run vg on the compacted graph

2. What did you want to happen?
I expect the count of snarls to be the same for both compacted and non-compacted graphs.

3. What actually happened?
The count of snarls reported reduces on compaction.

4. What data and command can the vg dev team use to make the problem happen?

Input GFA:

S	A	*	LN:i:100
S	B	*	LN:i:100
S	C	*	LN:i:100
S	D	*	LN:i:100
S	F	*	LN:i:100
S	G	*	LN:i:100
S	H	*	LN:i:100
S	I	*	LN:i:100
S	J	*	LN:i:100
S	K	*	LN:i:100
L	A	+	B	+	0M
L	A	+	B	-	0M
L	B	-	C	-	0M
L	B	+	C	-	0M
L	C	-	D	+	0M
L	C	-	F	+	0M
L	D	+	G	-	0M
L	F	+	G	-	0M
L	G	-	H	+	0M
L	G	-	I	+	0M
L	H	+	K	+	0M
L	K	+	K	+	0M
L	H	+	J	+	0M
L	I	+	J	+	0M
L	B	-	A	-	0M
L	B	+	A	-	0M
L	C	+	B	+	0M
L	C	+	B	-	0M
L	D	-	C	+	0M
L	F	-	C	+	0M
L	G	+	D	-	0M
L	G	+	F	-	0M
L	H	-	G	+	0M
L	I	-	G	+	0M
L	K	-	H	-	0M
L	K	-	K	-	0M
L	J	-	H	-	0M
L	J	-	I	-	0M

Commands used:

vg convert -g "$INPUT_GFA" > "$FILE.vg"
vg mod -n "$FILE.vg" > "${FILE}_mod.vg"

vg index -x "$FILE.xg" "$FILE.vg"
vg index -x "${FILE}_mod.xg" "${FILE}_mod.vg"

vg snarls -a -m 1000 "$FILE.xg" > "$OUT.snarls"
vg snarls -a -m 1000 "${FILE}_mod.xg" > "${OUT}_mod.snarls"

vg view -j -R "$OUT.snarls" > "$OUT_snarls.json"
vg view -j -R "${OUT}_mod.snarls" > "${OUT}_mod_snarls.json"

Output:

OUT_snarls.json

{"directed_acyclic_net_graph": true, "end": {"backward": true, "node_id": "3"}, "end_self_reachable": true, "start": {"node_id": "1"}, "start_end_reachable": true, "start_self_reachable": true}
{"directed_acyclic_net_graph": true, "end": {"backward": true, "node_id": "6"}, "start": {"backward": true, "node_id": "3"}, "start_end_reachable": true, "type": 1}
{"end": {"node_id": "9"}, "start": {"backward": true, "node_id": "6"}, "start_end_reachable": true}

OUT_mod_snarls.json

{"end": {"node_id": "3"}, "start": {"backward": true, "node_id": "2"}, "start_end_reachable": true}

5. What does running vg version say?

vg version v1.61.0 "Plodio"
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

Kindly look into this!

Thanks