Estimate LD based on Pan-UKB routine

[biona001]

Now estimate_sigma follows the routine of Pan-UKB LD estimation, which also handles covariate adjustments. We no longer use the shrinkage-based method.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 37.83784% with 23 lines in your changes missing coverage. Please review.

Project coverage is 63.17%. Comparing base (634b8a0) to head (b548ca6).

Files with missing lines	Patch %	Lines
src/make_hdf5.jl	46.66%	16 Missing ⚠️
src/app.jl	0.00%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #37      +/-   ##
==========================================
- Coverage   64.73%   63.17%   -1.56%     
==========================================
  Files           5        5              
  Lines         689      717      +28     
==========================================
+ Hits          446      453       +7     
- Misses        243      264      +21     

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