S4 cleanup

[danielnachun]

This is the big PR. I'll have more details on this elsewhere but I will merge now if this works.

[codecov]

Codecov Report

❌ Patch coverage is 84.56111% with 547 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.23%. Comparing base (832c667) to head (b2925db).

Files with missing lines	Patch %	Lines
R/fineMappingPipeline.R	81.39%	144 Missing ⚠️
R/causalInferencePipeline.R	74.74%	98 Missing ⚠️
R/colocboostPipeline.R	77.74%	79 Missing ⚠️
R/QtlDataset.R	85.28%	68 Missing ⚠️
R/genotypeIo.R	87.65%	59 Missing ⚠️
R/colocPipeline.R	81.19%	44 Missing ⚠️
R/gwasSumStats.R	82.35%	15 Missing ⚠️
R/allGenerics.R	87.80%	10 Missing ⚠️
R/GenotypeHandle.R	92.38%	8 Missing ⚠️
R/FineMappingEntry.R	89.85%	7 Missing ⚠️
... and 7 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #521      +/-   ##
==========================================
- Coverage   83.70%   83.23%   -0.48%     
==========================================
  Files          51       57       +6     
  Lines       13007    13760     +753     
==========================================
+ Hits        10888    11453     +565     
- Misses       2119     2307     +188     

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.