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switch to cpp11 and fix enloc bugs#474

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danielnachun merged 7 commits intomainfrom
cpp11-genotypes
Apr 21, 2026
Merged

switch to cpp11 and fix enloc bugs#474
danielnachun merged 7 commits intomainfrom
cpp11-genotypes

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@danielnachun
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This PR is a major update with several important changes:

  • I have switched from Rcpp to cpp11. cpp11 is a more modern interface for C++ in R developed by the tidyverse team. It nicely cleans up our code and should make compilation easier
  • I verified our C++ ports with the upstream code using Claude and nothing needed to be changed except for a few small bugs with the enloc QTL enrichment
  • We now have proper test fixtures for our basic genotype handling functions
  • These test functions have now allowed us to make all of the genotype handling functions fully generic across .bed/.bim/.fam, .pgen/.pvar/.psam, VCF and GDS.

The only test fixtures I think we need to add are:

  • TWAS weights
  • multitrait summary statistics RDS (for mashr)
  • susie fit RDS
  • tensorQTL summary statistics
  • stochastic genotypes

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codecov Bot commented Apr 21, 2026

Codecov Report

❌ Patch coverage is 82.01439% with 100 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.34%. Comparing base (0517999) to head (6b9fc06).
⚠️ Report is 1041 commits behind head on main.

Files with missing lines Patch % Lines
src/dentist_iterative_impute.cpp 41.53% 38 Missing ⚠️
src/qtl_enrichment.hpp 67.41% 29 Missing ⚠️
R/file_utils.R 90.31% 25 Missing ⚠️
R/LD.R 88.00% 3 Missing ⚠️
R/mash_wrapper.R 0.00% 2 Missing ⚠️
src/sdpr_mcmc.cpp 66.66% 2 Missing ⚠️
src/lassosum_rss.cpp 96.55% 1 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##             main     #474       +/-   ##
===========================================
+ Coverage   27.48%   88.34%   +60.85%     
===========================================
  Files          32       35        +3     
  Lines        4377     6906     +2529     
===========================================
+ Hits         1203     6101     +4898     
+ Misses       3174      805     -2369     

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@danielnachun danielnachun merged commit 4cfc55e into main Apr 21, 2026
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