Option to download displayed portion of the track files?

[taprs]

Is your feature request related to a problem? Please describe.

We want to publish a big VCF file. There will be a Jbrowse2 instance, and we plan to add a way to query the VCF by region to let users download a small portion of the data.

Describe the solution you'd like

Since the VCF file is anyway queried by index by Jbrowse 2 when displayed, I was wondering if this displayed portion of the track can be made downloadable. I guess it could be a generic solution for all indexed tracks.

Describe alternatives you've considered

The alternative is to do querying outside Jbrowse2, maybe firing up a Galaxy instance with bcftools or thinking of a new interface to it.

[cmdcolin]

this is a good idea. there is some question of exactly what is needed

there can be multiple approaches

a) minimal processing e.g. just return the raw lines from a tabix request to the genomic range. probably needs vcf header too. for most cases this works well, but sometimes e.g. in the case of gff3, it can return partial features if not careful.
b) add feature processing e.g. our adapters run getFeatures, return features in a json format, and then we convert back to the data lines.

previous attempt here, i have tried to keep it up to date with latest main but it hasn't gotten into a merge ready state and doesn't really do VCF and is more in the (b) family of choices #3439 this one was particularly complicated because they wanted genbank format which is a very odd format to 'convert to'

[taprs]

Thanks for the heads up! I was rather thinking of option a) because it seems most straightforward and broadly applicable; GFF with its hierarchical structure might be a problem indeed but maybe just outputting what indexing gives you + the header would be enough?.. I mean, one would see a truncated feature on the screen as well...