Jonathon LeFaive

Is there a reason why BLAS is not available during the appveyor test? Should BLAS and LAPACK be optional?

I see. This is not an issue with conda as they set placeholder prefix paths when building and then do a string replace when users run `conda install` (see https://stackoverflow.com/a/65136313/1034772)....

Both target_link_libraries() and target_compile_features() are supposed to be in the lists file (not the config file). I created a PR (#193) to resolve this.

Some thoughts: 1. I doubt this proposed update is going help much with Minimac4. In my experience, the biggest IO bottleneck that exists in Minimac4 is from writing temp files,...

This message is referring to the `Sites(GWAS/Ref/%)` column in the log. If there aren't enough sites in your array data (labeled GWAS) compared to the reference panel (labeled Ref), then...

Thanks for reporting this. I just pushed some fixes for this (200dfe721a5bdf40c7e0af3bfbb4c2d66970e530 and f79b38b336adbef782e17a7d7cde52808da3d939). Please try the latest from master.

This should be fixed in v3.4.2 (https://github.com/statgen/EPACTS/releases/tag/v3.4.2).

Newer versions use Cmake instead of Autotools. See build instructions in [readme](https://github.com/statgen/EPACTS/blob/v3.4.2/README.md).

Remove `python -m`. It should be `cget install -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC" -f requirements.txt`. You may need to install cget beforehand with `pip install cget`.

The bin path in which cget is installed probably isn't in your PATH environment variable. There's a good chance that it is located at `~/.local/bin/cget`. If not, running `pip3 uninstall...