Christopher Chang

Yes, there's technically one part of the .pgen format that has not been fleshed out yet (multiallelic dosages), but that part is unimportant for most applications. I will work on...

Ended up being delayed by far more than a weekend, but pgenlibr is now on CRAN.

Some REF/ALT alleles are swapped in at least one of your VCFs. If you don't have any indels, the --ref-from-fa flag can be used to repair the problem VCF. Otherwise,...

I will try to make a basic writer available within the next month. What type of data are you working with (any phase or dosage info)?

Thanks for reporting this. --bmerge is not symmetric; the first appearance of a variant has priority when there are duplicates, and I can't change this behavior without breaking backward compatibility....

In principle, yes, but realistically you are better off saving yourself several months of work and instead checking for plink2 error code 13 ("DegenerateData").

I am open to a much-more-manageable pull request that tweaks the VCF/BCF(/other?) import functions so that they return that error code on an empty input file; I'll try to take...

The issue is that 0 variants is an uninteresting edge case that nevertheless would need to be handled correctly by every single plink2 function when —allow-no-vars is reintroduced. Development of...

No, and this isn't likely to change soon; use other software for this. Maybe several years down the line, though.

plink2 normally excludes "nonfounders" (i.e. any sample with parental IDs listed in the .fam/.psam file) from its MAF calculation. This results in small MAF differences from other programs which don't...