vcfLink in R 4.1

[jdalapicolla]

Dear Dr. Pope,

I'm Jeronymo and I use and cite your package, it's very useful. Currently, I'm migrating my scripts to R 4.1 and I found some incompatibilities with r2vcftools. I would like to know if you are already aware of it and if there is any proposal for a package/function update.

Previously, I used R 3.6.3 and (the version of VCFtools in both R is the 0.1.17 - Mar 2020). My old vcfs (made with R 3.6.3) load normally into R 4.1 using the vcfLink function. But when I make a new subset or use another function/analysis with r2vcftools, there are a warning:

Warning: Expected at least 2 parts in INFO entry: ID=DP4,Number=4,Type=Integer,Description="Ref+, Ref-, Alt+, Alt-">

Reading in the vcftools forum, I found this: "It's just a warning that vcftools doesn't know how to handle the comma within the Description tag. If you remove that comma in the description, the warning will go away. Otherwise, it can generally be ignored." Link

I ignored it and continued my script, I saved a subset of this vcf and when I tried to open it again in R 4.1 with the vcfLink function the scan() function gave an error. In R 3.6.3 this error did not happen.

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
 line 1 did not have 11 elements

I believe it must be an error due to that comma in the description tag. I removed the entire vcf INFO block manually, and the without commas the vcf was read by the vcfLink function in R 4.1.

I would like to know if there is a more practical way to solve this issue without having to remove this part of vcf manually?

Thank you for your time,
Sincerely,
Jeronymo Dalapicolla