vg filter cannot detect nodes field from gam file

[cwatt]

1. What were you trying to do?
Extract nodes from a .gam file mapped using vg giraffe to a minigraph-cactus graph. See: https://github.com/vgteam/vg/wiki/Getting-alignment-statistics-with-vg-filter

2. What did you want to happen?
I wanted a .tsv file containing the nodes associated with each read.

3. What actually happened?
vg crashed because the node field was not detected in the .gam file. Below is a small portion of the very long error message:

Crash report for vg terminate called recursively
terminate called after throwing an instance of '━━━━━━━━━━v1.66.0 "Navetta"━std::runtime_error
terminate called recursively
terminate called recursively
━━━━━━━━━━━━━━━terminate called recursively
Caught signal 6 raised at address 0x22eebac; tracing with backward-cpp
━━━━━━━━━━━━━━━━━━━'
━  what():  error: Writing non-existent field to tsv: nodes
━━━━
Crash report for vg ━v1.66.0 "Navetta"
Caught signal 6 raised at address 0x22eebac; tracing with backward-cpp

However, the .json version of the .gam file clearly contains node ids. Example:

{"annotation": {"last_placed_stage": "none", "last_placed_stage_0bp": "none", "mapq_explored_cap": 230.56100035860723, "mapq_uncapped": 2147483647, "proper_pair": true, "secondary_scores": [161]}, "fragment_next": {"name": "seed_1_fragment_0_2"}, "identity": 1.0, "mapping_quality": 60, "name": "seed_1_fragment_0_1", "path": {"mapping": [{"edit": [{"from_length": 13, "to_length": 13}], "position": {"node_id": "109457256", "offset": "6"}, "rank": "1"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"node_id": "109457257"}, "rank": "2"}, {"edit": [{"from_length": 113, "to_length": 113}], "position": {"node_id": "109457259"}, "rank": "3"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"node_id": "109457260"}, "rank": "4"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"node_id": "109457261"}, "rank": "5"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"node_id": "109457262"}, "rank": "6"}, {"edit": [{"from_length": 4, "to_length": 4}], "position": {"node_id": "109457264"}, "rank": "7"}, {"edit": [{"from_length": 2, "to_length": 2}], "position": {"node_id": "109457265"}, "rank": "8"}, {"edit": [{"from_length": 3, "to_length": 3}], "position": {"node_id": "109457267"}, "rank": "9"}, {"edit": [{"from_length": 1, "to_length": 1}], "position": {"node_id": "109457268"}, "rank": "10"}, {"edit": [{"from_length": 11, "to_length": 11}], "position": {"node_id": "109457269"}, "rank": "11"}]}, "quality": "KCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKBgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoGBgYKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKCgoKA==", "score": 161, "sequence": "[REDACTED]", "time_used": 0.00070879700000000005}

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:

N/A

5. What data and command can the vg dev team use to make the problem happen?
vg filter --tsv-out "score;mapping_quality;nodes" mapped.gam > mapped-stats.tsv
I can't share this data. Any .gam file should work, I think.

6. What does running vg version say?

vg version v1.66.0 "Navetta"

Thank you!

[faithokamoto]

nodes was added in v1.68.0 as a field accessible via --tsv-out. You should probably update your vg version. Otherwise, you're stuck with converting things to JSON and then parsing that.

Alternatively, if you have a local build of vg, you could directly edit the code in the same way as the PR did: https://github.com/vgteam/vg/pull/4678/files