Unable to load feature tracks in linear syneny view

[Thys3Potgieter]

Describe the bug I am not able to select and visualize feature tracks in linear synteny view, but in linear genome view I can load tracks for the same assembly To Reproduce

1. Load linear synteny view

2. Select the PAF file

3. Click on "Open Track Selector" No tracks are shown to be available.

4. When using linear view, the tracks are available

Expected behavior I expect to see all available tracks in linear synteny view.

Version: (base) root@9e7f64a11a7d:/jbrowse/local/demo# jbrowse --version @jbrowse/cli/2.13.0 linux-x64 node-v20.5.1 and Fetching https://github.com/GMOD/jbrowse-components/releases/download/v2.13.0/jbrowse-web-v2.13.0.zip...

Additional context { "assemblies": [ { "name": "S507", "sequence": { "type": "ReferenceSequenceTrack", "trackId": "S507-ReferenceSequenceTrack", "adapter": { "type": "IndexedFastaAdapter", "fastaLocation": { "uri": "S507_comb_assmbly_18_03_16.fasta", "locationType": "UriLocation" }, "faiLocation": { "uri": "S507_comb_assmbly_18_03_16.fasta.fai", "locationType": "UriLocation" } } } }, { "name": "S5527", "sequence": { "type": "ReferenceSequenceTrack", "trackId": "S5527-ReferenceSequenceTrack", "adapter": { "type": "IndexedFastaAdapter", "fastaLocation": { "uri": "S5527_comb_assmbly_18_03_16.fasta", "locationType": "UriLocation" }, "faiLocation": { "uri": "S5527_comb_assmbly_18_03_16.fasta.fai", "locationType": "UriLocation" } } } } ], "configuration": {}, "connections": [], "defaultSession": { "name": "New Session" }, "tracks": [ { "type": "FeatureTrack", "trackId": "S5527_features.gff3.sorted.gff3", "name": "S5527_features.gff3.sorted.gff3", "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": "S5527_features.gff3.sorted.gff3.gz", "locationType": "UriLocation" }, "index": { "location": { "uri": "S5527_features.gff3.sorted.gff3.gz.tbi", "locationType": "UriLocation" }, "indexType": "TBI" } }, "assemblyNames": [ "S5527" ] }, { "type": "FeatureTrack", "trackId": "S507_features.gff3.sorted.gff3", "name": "S507_features.gff3.sorted.gff3", "adapter": { "type": "Gff3TabixAdapter", "gffGzLocation": { "uri": "S507_features.gff3.sorted.gff3.gz", "locationType": "UriLocation" }, "index": { "location": { "uri": "S507_features.gff3.sorted.gff3.gz.tbi", "locationType": "UriLocation" }, "indexType": "TBI" } }, "assemblyNames": [ "S507" ] }, { "type": "SyntenyTrack", "trackId": "S507_vs_S5527", "name": "S507_vs_S5527", "adapter": { "type": "PAFAdapter", "pafLocation": { "uri": "S507_vs_S5527.paf", "locationType": "UriLocation" }, "assemblyNames": [ "S507", "S5527" ] }, "assemblyNames": [ "S507", "S5527" ] } ] }

Please assist this PhD researcher to finish their thesis :) And thanks for the great tool!

[cmdcolin]

hi there, this was a bug in the v2.13.0 release. i made a hotfix on monday for it here https://github.com/GMOD/jbrowse-components/issues/4500

you can get the latest 'nightly' build with

jbrowse upgrade --nightly in your instance

I will probably release a formal patch version very soon also

[Thys3Potgieter]

Thank you for helping me (and not the first time :) Problem solved. cheers!

[cmdcolin]

I just made this an official release now also in v2.13.1 cause definitely don't want other people to run into this :)