optimize enloc and QC pipelines

[danielnachun]

In this PR, I have attempted to fix the bottlenecks in enloc (this will need real testing).

I also wanted to clean up the sumstats QC pipeline which was kind of messy because dentist, for example had a whole other function which would load data separately from our main loading functions. I have now removed all functions which try to load data outside of our main pipeline.

The GCTA correction for LD estimation has been moved into R and is now available for compute_LD

These functions were removed, so we should figure out, where if anywhere, the xQTL pipeline could depend on them so it can be updated:

• ctwas_bimfile_loader — loaded LD blocks from cTWAS bim files; replaced by ld_loader(LD_info=...)
• dentist_from_files — ran DENTIST end-to-end from file paths; replaced by composing load_genotype_region() + allele_qc() + compute_LD() + dentist()
• get_ctwas_meta_data — parsed cTWAS metadata; replaced by ld_loader(LD_info=...)
• parse_dentist_output — read output files from the DENTIST C++ binary
• read_dentist_sumstat — read DENTIST-format summary statistics files

[codecov]

Codecov Report

❌ Patch coverage is 97.05882% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 80.56%. Comparing base (0517999) to head (70f912d).
⚠️ Report is 1028 commits behind head on main.

Files with missing lines	Patch %	Lines
R/misc.R	93.75%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #469       +/-   ##
===========================================
+ Coverage   27.48%   80.56%   +53.08%     
===========================================
  Files          32       41        +9     
  Lines        4377     7760     +3383     
===========================================
+ Hits         1203     6252     +5049     
+ Misses       3174     1508     -1666     

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