I sent an email to Lincoln to see if he will sponsor one of us!
We have an embedded ReactLinearGenomeView. The component has a menu in the upper-right, which can have items added to it. Is there a way to inject another item into the menu bar itself? Specifically, because we show this viewer full-screen, I want to put some kind of button/link that is very obviously has the text "Return to Site".
could do that too
12 replies
Another question: I see your docs on themes, which works well. However, are more public examples of specific color combinations people have figured out work well? For example, is there a stock jbrowse blue theme, red theme, etc? Or perhaps examples of what color sets people have used?
Category for JBrowse abstract. submit in which category? "Application of bioinformatics to cancer biology” or "New software tools for data analysis”? I feel like it should be the former, since it doesn’t really do “analysis”, it just helps users look at stuff to do their own analysis. Anybody want to disagree?
Also, sorry working on this so late: it’s been a busy day and I had to take the dog to the vet which has really messed up my schedule.
added to cal:)
$ jbrowse add-assembly test_data/volvox/volvox.fa --out t1 --load copy
Added assembly "volvox" to t1/config.json
$ jbrowse add-track test_data/volvox/volvox-sorted.bam --indexFile=test_data/volvox/volvox-sorted.bam.csi --out t1 --load copy
Added track "volvox-sorted" to t1/config.json
$ ls -1 t1
config.json
volvox.fa
volvox.fa.fai
volvox-sorted.bam
volvox-sorted.bam.csi
using jbrowse cli 1.5.1
Maybe this line: https://github.com/GMOD/jbrowse-components/blob/24b45e29b681277e68ec088034f3ef25bb80c389/products/jbrowse-cli/src/commands/add-track.ts#L391 should be
index: index || ${fileName}.bai instead, like the part for bam?
this should get fixed
possible issue about estimating bytes downloaded, could be possibly a method for stats estimation GMOD/jbrowse-components#2251
Pangenome hackathon+talks Dec 9-10 https://twitter.com/erikgarrison/status/1465346595835326497?t=NnmbhvRONJYJoxYX16s9tg&s=19
it's free so why not
Hello - I'm hoping to get some advice. We're trying to make a plugin that filters variants in a VCF track based on whether specific samples are non-wild type. The logic is not hard (make sure the genotype of samples !== '"./." or "0/0"); however, has ~2500 samples. At least how we're doing this makes a very noticeable lag in loading. I experimented with pre-computing an array of the non-WT samples in the getFeatures() method of a custom VcfTabixAdapter; however, this code is called repeatedly whenever any rendering happens. Is there a place I could hook into the processing of VCF features that would let me efficiently pre-compute some information, and let that information persist? Alternately, is there another way I should think about approaching this problem?
that cache would be in the custom adapter
i can write an implementation sketch of it quickly, just a seec