Click to popup does not work in variant track with display mode collapsed

[alimanfoo]

Hi there, I'm using igv.js via the igv-notebook package (v0.2.1) and creating a browser with a variant track from an all sites VCF file. I like the collapsed display mode as it shows everything on a single line, but I notice that clicking on a variant or genotype then seems broken. It looks like the click areas are behaving as if the track was still in expanded mode. I infer this because clicking to create a popup seems to work for every other variant, and you can get a popup to work for every other one by clicking below the genotype (i.e., where it would appear if expanded display mode).

[jrobinso]

Yes, confirmed, its an igv.js bug.

[alimanfoo]

Thanks @jrobinso. I'm no javascript coder, but I had a bit of a browse around the source code, noticed that in VariantTrack.clickedFeatures() there doesn't seem to be any handling of the collapsed display mode.

Btw, my variants track has one SNP for every position (all sites) and one sample, and so looks like this with expanded display mode:

I'm looking for any way to get all variants displayed in a single row, as it looks with collapsed mode:

I also tried adding "maxRows": 1 to the track config, which from the code suggested that should limit the number of rows used during packing of features, but that didn't seem to do anything.

[jrobinso]

Yes its just a bug for sure, I think I've fixed it but can't test now as I'm traveling today.

[alimanfoo]

Thanks so much @jrobinso, look forward to the fix.

As an aside, I did wonder if the feature packing behaviour was quite right. In my case I have a SNP variant at every position, so lots of adjacent SNPs basically, but they don't actually overlap each other. So strictly speaking there is no need to use more than one row to display these, even in expanded display mode. Do you think that's worth raising as a separate issue?

[jrobinso]

I will look into that as part of this ticket. If you have a small vcf you can share it would save me the trouble of creating one.

[jrobinso]

OK both issues raise here are fixed in igv.js version 2.12.4, and igv-notebook version 0.2.2

[alimanfoo]

Hi @jrobinso, sorry I missed your comment above to share a small dataset, I'll make sure to do that up front next time. Thank you so much for the quick fix and release, super appreciated. I'm going to be using IGV for teaching next week and so having this simpler view of the SNPs makes the explanation much easier! 🙏

[jrobinso]

No problem, good luck with your course.