Standardize phred qual scaling between BAM and CRAM and add option to make mismatches render in a lighter color when quality is low

[cmdcolin]

This adds

(a) a new coloring option "Adjust mismatch visibility by quality" that helps adjust the coloring of SNPs by their qual score
(b) standardize the qual score across BAM and CRAM. the CRAM was adding +33 which is basically what is done to report proper ASCII characters for scores, but to be standardized we skip adding +33

[codecov]

Codecov Report

Merging #1720 (8d58cc5) into master (703b97e) will increase coverage by 0.01%.
The diff coverage is 81.48%.

@@            Coverage Diff             @@
##           master    #1720      +/-   ##
==========================================
+ Coverage   58.81%   58.83%   +0.01%     
==========================================
  Files         448      448              
  Lines       20754    20767      +13     
  Branches     4919     4922       +3     
==========================================
+ Hits        12207    12218      +11     
- Misses       8240     8242       +2     
  Partials      307      307              

Impacted Files	Coverage Δ
...lugins/alignments/src/LinearPileupDisplay/model.ts	73.93% <0.00%> (-0.91%)	⬇️
...ns/alignments/src/PileupRenderer/PileupRenderer.ts	65.87% <70.00%> (-0.11%)	⬇️
...lignments/src/BamAdapter/BamSlightlyLazyFeature.ts	79.24% <100.00%> (+0.39%)	⬆️
...lugins/alignments/src/BamAdapter/MismatchParser.ts	88.15% <100.00%> (+0.74%)	⬆️
...gnments/src/CramAdapter/CramSlightlyLazyFeature.ts	85.78% <100.00%> (+0.22%)	⬆️
packages/core/util/index.ts	82.20% <0.00%> (-0.33%)	⬇️
...inearGenomeView/components/RefNameAutocomplete.tsx	93.61% <0.00%> (+4.25%)	⬆️

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[rbuels]

but does this lead to the quality scores being all -33 in the feature details panel?

[cmdcolin]

Nope, the scores are reported as numbers in the range 0-93 or so when you add 33, you get it starting in the ascii range 33, the first printable character !, to 126, a ~ last printable http://www.asciitable.com/

So the only reason to add 33 is so that you can encode them into an ascii string

And with this change the "Color by per-base quality" and the feature detail panel qual score reports are the same for a BAM and CRAM file. Can see this in volvox examples (many tracks have both BAM and CRAM examples) and the human data (HG002 ultralong BAM and CRAM exist)