Adds URL query param for highlight on LGV

[carolinebridge]

Responds to comments on #2316 and #599 requesting a highlight feature similar to what existed in JB1.

Allows a user to specify a highlight region in the URL with the pattern &highlight=REF:START..END

[carolinebridge]

First draft divorced from existing bookmarking functionality -- adds a highlight element to the LGV if provided in the URL params.

[codecov]

Codecov Report

Attention: Patch coverage is 28.37838% with 53 lines in your changes are missing coverage. Please review.

Project coverage is 62.62%. Comparing base (ff057f5) to head (3da45d3).
Report is 9 commits behind head on main.

Files	Patch %	Lines
...view/src/LinearGenomeView/components/Highlight.tsx	35.89%	25 Missing ⚠️
.../LinearGenomeView/components/OverviewHighlight.tsx	9.52%	19 Missing ⚠️
...ar-genome-view/src/LaunchLinearGenomeView/index.ts	28.57%	5 Missing ⚠️
...c/LinearGenomeView/components/OverviewScalebar.tsx	33.33%	1 Missing and 1 partial ⚠️
...s/linear-genome-view/src/LinearGenomeView/model.ts	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4234      +/-   ##
==========================================
- Coverage   62.71%   62.62%   -0.09%     
==========================================
  Files        1084     1086       +2     
  Lines       31316    31390      +74     
  Branches     7474     7502      +28     
==========================================
+ Hits        19639    19658      +19     
- Misses      11503    11557      +54     
- Partials      174      175       +1     

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[cmdcolin]

there may want to be a system to clear the highlights. in jbrowse 1. in jbrowse 1 there was sort of a 3-state button that helped with this. not sure the best UI for it for jbrowse 2, it is possible it doesn't need to be so "present" on the header bar and could instead be that clicking on the highlight itself could clear it or something like that. just an idea

additionally, it may be useful to show the highlight in the overviewscalebar

can see example for jbrowse 1 here

https://jbrowse.org/code/JBrowse-1.16.11/?loc=ctgA%3A9897..32106&tracks=DNA&data=sample_data%2Fjson%2Fvolvox&tracklist=1&highlight=ctgA%3A18821..28852&nav=1&overview=1

[carolinebridge]

Demo: https://s3.amazonaws.com/jbrowse.org/code/jb2/query-param-region/index.html?config=test_data/volvox/config.json&assembly=volvox&loc=ctgA:1-7000&tracks=volvox_sv_test,variant_effect_demo_jannovar&highlight=ctgA:2007-2993

[cmdcolin]

I added a commit that avoids the highlight not rendering if the coordinate was numeric 0 (explicit checks for undefined) here 9c93a5a

would actually be nice if there was a lint rule for this as it can be so easy to miss this type of bug (you can reproduce numeric 0 by highlighting something starting at coord 1 e.g. ctgA:1-100 since it gets changed to 0 on import due to 1 base to 0 base conversion)

[cmdcolin]

found the lint rule :) #4238

[cmdcolin]

i believe this cast is "not valid", as model.highlight.start and model.highlight.end are potentially undefined by definition of ParsedLocString(?)

[carolinebridge]

Most recent commit: is making use of Required https://www.typescriptlang.org/docs/handbook/utility-types.html#requiredtype satisfactory?

[cmdcolin]

that is an interesting new feature of typescript, but I might opt for creating a new type (just the simple {assemblyName:string,refName:string,start:number,end:number} instead perhaps, and try to avoid using "as" cast entirely (casts are generally best if avoided as it cancels out any check that typescript would do for you)

[cmdcolin]

I believe this cast may not be valid, as refName is required on ParsedLocString. potentially, making it something like {assemblyName:string,refName:string,start:number,end:number}|undefined might be better than parsedlocstring, because then you know you have all required fields, or else it is just undefined

[cmdcolin]

with above comment, can make it "|undefined" so that undefined clears it

[cmdcolin]

should be good for now, can see how it goes:)

[cmdcolin]

can you add a note to urlparams.md mentioning it? also might mention that it must be combined with &loc and &assembly because otherwise the app does not realize it is doing the "simple lgv launcher mode"

[grexor]

This works great and thank you all, Jbrowse is amazing. I am now usign the highlight feature extensively and a need to highlight several regions somehow appeared. Do you think it would be possible to implement something like it? (or should I also have a look and perhaps can help?)

I was thinking something in this direction:

&highlight=1:100..200,1:250..300

This would highlight two regions on ref. 1 and 2, coordinates 100-200 and 250-300.

Any help appreciated, Thanks, Gregor

[cmdcolin]

@grexor I just created a new issue for this here !