Legend state / samples checked not stored when modifying configuration

[maxm4]

Hello,

I find your tool very useful for visualizing genome graph alignments computed for instance with Cactus and converted to .vg.
However, Cactus requires in input a Newick tree and generates 'fake' sequences for common ancestors.

This means that when visualizing my sample genomes I also have 'fake' ancestral genomes which I am not interested in.
In SequenceTubeMap I then uncheck all of the ~20 ancestral genomes from the 'Legend' so that the associated tracks are not displayed.
This works well, until I make any modification to the configuration, i.e. changing the reference, the region displayed, removing variants or node sequences, where then everything becomes checked again.

Unchecking all of the genomes manually is very tedious, would it be possible to store durably the legend configuration in the javascript backend? It would be nice to keep the state of how the samples are checked/unchecked for as long as the data itself (the .vg) is not changed.

Thank you very much in advance,
Maxime

[adamnovak]

We don't currently persist the visible path selection, but we should.

For your specific case, if you never want to see these paths, you could try removing them from the graph with:

vg paths --drop-paths --paths-file list-of-paths.txt -x old.vg >new.vg

That would give you a .vg file that does not have the paths you do not care about, and then you could visualize just the remaining paths in the tube map by using that file.