Create method to collapse introns in LGV

[cmdcolin]

Collapsed introns or collapsed other regions would result results in a big change in coordinates. The refName labeling would could be modified to allow it to display a more complete description of the displayed region instead of just the refName.

[rbuels]

Implementation idea so far is to make the ruler of a displayed region just be its locstring label or similar thing, if the displayed region is narrow enough on the screen that there isn't room for meaningful ruler ticks in its ruler.

[cmdcolin]

Somewhat related #1084

[cmdcolin]

I retitled this to be a more generic intron collapsing issue

I made a demo where I manually stitched together some displayedRegions from the set of exons from one transcript in a gene (with 100bp on each side)

https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=local-YuIbRHX9y

It looks ok, it is pretty moderate in terms of total number of displayedRegions though so if there are e.g. 30-100 exons it would probably start looking messier and create ellided blocks, but that might be ok since you can zoom in on them

[cmdcolin]

script to stitch it together

run in devtools after clicking a feature

getSnapshot(JBrowseSession).widgets.baseFeature.finalizedFeatureData

copy output to test.json, then make nodejs script

const fs = require('fs')
const obj = JSON.parse(fs.readFileSync('test.json'))
const refName = obj.refName
const res = obj.subfeatures
  .filter(f => f.type === 'exon')
  .map(f => ({
    refName,
    start: f.start - 100,
    end: f.end + 100,
    assemblyName: 'hg19',
  }))
res.sort((a, b) => a.start - b.start)
console.log(res)

then copy output to clipboard

node test.js|pbcopy

then in devtools

JBrowseSession.views[0].setDisplayedRegions(<hit paste>)

[carolinebridge]

From meeting:

• right click gene collapse introns
• mouseover the hard black bar interregion lines
• open LGV region with collapse in a separate view maybe
• could make its own view that extends the LGV
• or just have a dialogue with collapsing options

[cmdcolin]

This feature may benefit from being implemented alongside the canvas feature renderer. The floating labels don't work well on with the SvgFeatureRenderer with the many discontinous regions and the Svg exports are messy too. Each could potentially be fixed within the current SvgFeatureRenderer framework, but i do think a new feature renderer is a good investment