@cmdcolin on #2554 you said something interesting I hope you could expand on here. you mention lazy parsing of genotypes. As noted above, we have a VCF with ~2400 samples. We previously never had code that did anything with samples until the details panel was opened. We are trying to implement code that lets the user filter sites based on specific samples having non-WT genotypes, and so we're starting to access genotype data much earlier and do this for all variants. What governs whether genotypes are parsed or not?
with #2554 , if you were accessing the genotypes for filtering, it would parse the genotypes but would not necessarily serialize to json
(binary vcf format)
@bbimber if you have the adapter config, you can get the raw header string with our "CoreGetInfo" RPC call, example here: https://github.com/GMOD/jbrowse-components/blob/1d22d290b8974ad21f7ddf8787db10f631d05d8f/packages/core/ui/AboutDialog.tsx#L48-L51. A feature will also have the VCF header data stored in it that you can access, example for INFO here: https://github.com/GMOD/jbrowse-components/blob/00c4e05cca8d054ab3456423b43e1bbd0e24be8c/plugins/variants/src/StructuralVariantChordRenderer/ReactComponent.js#L32-L36
I’ll delete it
and a embedded instance here http://portugalfishomics.ciimar.up.pt/app/scombercolias/
Hey - i have a question on plugin config. We have a plugin that lets a user choose a custom coloring scheme. This include a custom renderer. By default, renders support the property 'color1', which can be JEXL to set feature color. Our custom renderer has another simple string property called 'palette'. If palette is non-null, we run code that takes that string, builds a JEXL expression, and then sets color1. This works fine if the user picks that interactively. However, I'd like to hook into somewhere such that if the initial rendererConfig JSON has 'palette', we execute code to set color1 right away. Is there a point where I can hook to add this kind of code?
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Another question: our user base seems to have a hard time recognizing the track selector icon (we're using ReactLinearGenomeView). Has anyone encountered this and/or looked into more obvious ways to signal to users what to do? In our case, we load with one track pre-displayed, so there isnt the central 'Open Track Selector' button. For comparison, in JBrowse 1 the side panel was considerably more obvious
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For anyone interested, here is a link to the jbrowse-jupyter https://github.com/GMOD/jbrowse-jupyter/tree/docs. All feedback is welcomed.
also, the tutorial for ismb says it's not generally used for presenting a specific software https://www.iscb.org/ismb2022-submissions/tutorials
i was also surprised too see a relatively shortlist of tutorials! In previous years, their had been more.
Also, we re-export mobx, mobx-state-tree, react, material-ui, and others for plugins to use, so if we upgrade them we risk breaking plugins. Those breaking changes may have to happen someday, but we'll have to plan for it.
docs for the d4 format now say it has some support for static http requests https://github.com/38/d4-format#reading-d4-file-served-by-static-http-server
i do want to try to make more progress on the pag workshop if possible. i dunno
Hey - I wanted to re-ask a question from earlier: does anyone have suggestions on coaxing an embedded LGV to make itself full page height? This would both be aesthetically preferable to us (otherwise we just have this white space), and at least in our hands it doesnt reliably auto-expand itself. The user can manually drag to open it, but that's not ideal here. Thanks for any ideas.
@bbimber if you have a link that shows what you mean by not autoexpanding it may be useful
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That screenshot is related to the thread above about autoexpanding LGV