Draw SNPs in modifications/methylation views

[cmdcolin]

Instead of drawing colorful SNPs, in the modifications view, this proposes that the SNPs be drawn in a simpler black on white

Would be curious if you had any feedback on this design @gringer xref https://twitter.com/gringene_bio/status/1527797881234931712

Example screenshot with this branch

The resulting SNPs look pretty similar to deletion boxes but not exactly the same

[cmdcolin]

when zoomed out it can look like this, with stretches of black. i don't want the black to overpower the main point of the plot which is the red modifications. could also hide them completely at higher zoomed out levels

[codecov]

Codecov Report

Merging #3001 (87cd8e8) into main (87269a6) will decrease coverage by 0.77%.
The diff coverage is 80.00%.

❗ Current head 87cd8e8 differs from pull request most recent head ff0165f. Consider uploading reports for the commit ff0165f to get more accurate results

@@            Coverage Diff             @@
##             main    #3001      +/-   ##
==========================================
- Coverage   61.56%   60.79%   -0.78%     
==========================================
  Files         591      584       -7     
  Lines       26986    26573     -413     
  Branches     6529     6432      -97     
==========================================
- Hits        16613    16154     -459     
- Misses      10076    10112      +36     
- Partials      297      307      +10     

Impacted Files	Coverage Δ
...s/alignments/src/PileupRenderer/PileupRenderer.tsx	49.39% <80.00%> (-0.81%)	⬇️
plugins/dotplot-view/src/DotplotReadVsRef.ts	0.00% <0.00%> (-71.80%)	⬇️
...ns/dotplot-view/src/DotplotView/components/util.ts	22.72% <0.00%> (-63.64%)	⬇️
plugins/dotplot-view/src/util.ts	1.69% <0.00%> (-59.33%)	⬇️
...ew/src/LinearSyntenyView/components/ImportForm.tsx	2.56% <0.00%> (-33.34%)	⬇️
...s/dotplot-view/src/DotplotView/components/Axes.tsx	55.38% <0.00%> (-32.31%)	⬇️
...mparativeView/components/LinearComparativeView.tsx	69.44% <0.00%> (-25.00%)	⬇️
...inearGenomeView/components/SearchResultsDialog.tsx	49.05% <0.00%> (-22.65%)	⬇️
...otplot-view/src/DotplotRenderer/DotplotRenderer.ts	61.41% <0.00%> (-18.12%)	⬇️
...ns/alignments/src/AlignmentsFeatureDetail/index.ts	83.33% <0.00%> (-16.67%)	⬇️
... and 232 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 87269a6...ff0165f. Read the comment docs.

[gringer]

SNPs in a single colour would be fine. Interested users can hover over the location to get more information.

It'd be helpful if they're distinguishable from insertions and deletions; could you make the SNP colours blue instead of black?

[cmdcolin]

Instead of drawing any background color, this now just draws the letters in black the reads, so should be helpful as long as you are zoomed in close enough to see letters.