sortAlleles

[Moriah Cohen]

sortAlleles uses alakazam's getAllele function with the default parameter "strip_d = TRUE". However, when sorting the "allele_groups" variable in findNovelAlleles using the sortAlleles function the script crashes each time there is a duplicate gene (with "D" - like IGHV2-70D*04) because it removes the "D" and creates an NA in the allele_groups variable .

allele_groups = allele_groups[sortAlleles(names(allele_groups))]

I have changed the default use of getAllele of the "strip_d" argument, reinstalled and it seems to solve it. I was wondering if there is a more straight forward solution.

Thanks

[Daniel Gadala-Maria]

I have updated getAllele to include strip_d=FALSE (which was previously not needed); this should fix it!