Add stats estimation to JB2

[peterkxie]

Add general and specific stats estimation to JBrowse 2, calculates the feature density to potentially limit the loading of tracks. BAM and Tabix files use the index to calculate their feature density

[peterkxie]

want to discuss timing issues in meeting, stats estimation makes a lot of tests flaky since it takes extra time, solution seems to be increasing timeout but i'd be increasing a lot of test timeouts

[cmdcolin]

can you link the demos showing how this works and provide some analysis of it's behavior on various files?

[codecov]

Codecov Report

Merging #2497 (6eb48ef) into main (abedfa8) will increase coverage by 0.16%.
The diff coverage is 81.97%.

@@            Coverage Diff             @@
##             main    #2497      +/-   ##
==========================================
+ Coverage   60.70%   60.86%   +0.16%     
==========================================
  Files         547      547              
  Lines       25579    25732     +153     
  Branches     6042     6080      +38     
==========================================
+ Hits        15528    15663     +135     
- Misses       9725     9743      +18     
  Partials      326      326              

Impacted Files	Coverage Δ
packages/core/util/stats.ts	96.00% <ø> (ø)
...ments/src/LinearAlignmentsDisplay/models/model.tsx	69.66% <0.00%> (ø)
...alignments/src/LinearPileupDisplay/configSchema.ts	100.00% <ø> (ø)
...lugins/alignments/src/LinearPileupDisplay/model.ts	63.58% <ø> (ø)
...rc/LinearSNPCoverageDisplay/models/configSchema.ts	100.00% <ø> (ø)
plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts	76.92% <0.00%> (-6.42%)	⬇️
...earDisplay/models/baseLinearDisplayConfigSchema.ts	100.00% <ø> (ø)
...genome-view/src/LinearBasicDisplay/configSchema.ts	100.00% <ø> (ø)
plugins/wiggle/src/WiggleRPC/rpcMethods.ts	54.05% <0.00%> (ø)
products/jbrowse-img/src/renderRegion.js	0.00% <0.00%> (ø)
... and 14 more

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[cmdcolin]

volvox filtered vcf track

the volvox filtered vcf track doesn't have very many features...i think ideally, it would not hit any feature density limit?

[cmdcolin]

here is the link to make the feature density calculation proportional to current zoom level https://github.com/GMOD/jbrowse/blob/dev/src/JBrowse/View/Track/CanvasFeatures.js#L260-L261

the "scale" is equal to 1/bpPerPx

[rbuels]

I'm betting the tests won't have to do as many clicks of "Force" now that it's accounting for scale

[cmdcolin]

if I turn on a bam or cram track e.g. viewing the entirety of chr1 it tries to download the entirety of chr1 and crashes

here it is for bam. the pileup subtrack appears to succeed but the snpcoverage track tries to end up downloading stuff anyways. i think for cram, it does not have e.g. the linecount heuristic and tries to download the entirety of chr1 for both snpcov and pileup

[cmdcolin]

might suggest putting in draft a bit more, just for more testing and such

[peterkxie]

ill look into this more, thanks for the details + screenshot