Loading PVAR in pgenlibr

[GabrielHoffman]

I'm working on an R package that reads PGEN files and performs statistical analysis in C++ via Rcpp (#283). pgenlibr provides almost everything a user needs.

The R function pgenlibr::NewPvar() to load a .pvar file calls LoadMinimalPvar() in C++:

plink-ng/2.0/pvar_ffi_support.cc

Line 64 in 6287f6a

PglErr LoadMinimalPvar(const char* fname, MinimalPvar* mpp, char* errstr_buf) {

It loads ID, REF and ALT, but not CHR or POS.

Do you have code to include chromosome and position information, so a user can intersect the variants with a BED file of genome intervals?

I'd do this myself, but that function is very hard to follow, and I'd write a new version but I'm concerned that there are some .pvar values it wouldn't parse correctly.

Best,
Gabriel

[chrchang]

This wasn't present in the first released version of pgenlibr since --set-all-var-ids provided a simple way to work around the limitation, but okay, now it's embarrassing. I will add this sometime in the next two weeks.