Change Alignments track "Fade mismatches by quality" setting to a separate config param and made it less strict

[cmdcolin]

The "Color by" scheme for alignments currently has 'Fade mismatches by quality'

Instead of making this specifically a property of "Color by", I change this to a separate setting

Then I also make the fading less "strict" e.g. right now it is a scale on a 0-90 but I make it on 0-50 because at quality 40, you are 99.99% sure the base call is right (see https://learn.gencore.bio.nyu.edu/wp-content/uploads/2018/01/Screen-Shot-2018-01-07-at-1.36.09-PM-768x535.png) and so you really only need to worry at like 20 or less. Even though phred can go up to 90 it does not need to really be faded after 50 or so I think

[cmdcolin]

this is also listed as true by default here, could consider turning off by default though

[codecov]

Codecov Report

Merging #1861 (7c53b5c) into main (1ed6ae8) will decrease coverage by 0.01%.
The diff coverage is 50.00%.

@@            Coverage Diff             @@
##             main    #1861      +/-   ##
==========================================
- Coverage   59.18%   59.17%   -0.02%     
==========================================
  Files         460      460              
  Lines       21402    21408       +6     
  Branches     5024     5026       +2     
==========================================
+ Hits        12667    12668       +1     
- Misses       8428     8433       +5     
  Partials      307      307              

Impacted Files	Coverage Δ
...lugins/alignments/src/LinearPileupDisplay/model.ts	68.42% <37.50%> (-0.61%)	⬇️
...ns/alignments/src/PileupRenderer/PileupRenderer.ts	65.65% <100.00%> (ø)
plugins/alignments/src/BamAdapter/BamAdapter.ts	69.51% <0.00%> (-1.22%)	⬇️
...ments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts	94.16% <0.00%> (-0.84%)	⬇️

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[cmdcolin]

Actually just made it off by default. it's on by default in igv but it's a little niche and could be unexpected