Optimizations for alignments tracks and BAM parsing

[cmdcolin]

This is a little microoptimization for the BAM/CRAM parsing pipeline

1. Skip "uniqifying" the mismatches, which is not needed if we don't add deletions from the MD string into the mismatches array (then deletions only come from CIGAR) string
2. Instead of generating the MD string, just get single bp mismatches if MD string not there
3. Bump @gmod/bam for Restore chunk cache for speed improvements bam-js#89
4. Avoids true canvas measureText for estimated measuretext from jbcore, which is faster
5. Precalculates contrast text colors for base text labels
6. Less rxjs abort checks and streaming, sncoverage adapter

[codecov]

Codecov Report

Merging #2809 (9b50144) into main (f8528c7) will decrease coverage by 0.04%.
The diff coverage is 57.57%.

@@            Coverage Diff             @@
##             main    #2809      +/-   ##
==========================================
- Coverage   60.00%   59.95%   -0.05%     
==========================================
  Files         584      584              
  Lines       26620    26505     -115     
  Branches     6464     6429      -35     
==========================================
- Hits        15974    15892      -82     
+ Misses      10332    10299      -33     
  Partials      314      314              

Impacted Files	Coverage Δ
packages/core/util/index.ts	85.18% <ø> (ø)
plugins/alignments/src/BamAdapter/configSchema.ts	100.00% <ø> (ø)
...nce/src/IndexedFastaAdapter/IndexedFastaAdapter.ts	81.25% <ø> (ø)
plugins/alignments/src/BamAdapter/BamAdapter.ts	74.74% <33.33%> (+0.49%)	⬆️
...ments/src/SNPCoverageAdapter/SNPCoverageAdapter.ts	58.49% <41.12%> (+1.52%)	⬆️
...gableElementTypes/renderers/FeatureRendererType.ts	74.00% <71.42%> (-1.48%)	⬇️
...lugins/alignments/src/BamAdapter/MismatchParser.ts	89.10% <89.65%> (+4.26%)	⬆️
packages/core/data_adapters/BaseAdapter.ts	74.39% <100.00%> (+6.25%)	⬆️
packages/core/util/tracks.ts	75.30% <100.00%> (+0.30%)	⬆️
...lignments/src/BamAdapter/BamSlightlyLazyFeature.ts	81.25% <100.00%> (+5.05%)	⬆️
... and 9 more

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[cmdcolin]

this had a tricky error in the full build (can be seen in the many red "X" on the builds before the latest build) that was tricky to debug. I think it gave an error from tsdx's version of typescript which is older.

[cmdcolin]

fixed now though

[cmdcolin]

I also removed a microptimization that was in the original PR for parsing cigar strings (avoided regex). it was somewhat faster on chrome but didn't strongly impact any jb2profile results for example. it is also slower on firefox. keeping track of some fun microbenchmarks here https://gist.github.com/cmdcolin/ef57d2783e47b16aa07a03967fd870d8

[cmdcolin]

~30% faster than main on 1000x longreads (2kb region viewed)
~30% faster than main on 2400x shortreads (2kb region viewed)
~250% faster (2.5x faster) on 2400x shortreads (100bp region viewed)

some tests here https://github.com/cmdcolin/jb2profile
this branch is jb2 v1.6.7+optim