If I have a genome with numeric chromosomes, then other non-MT scaffolds that aren't numeric, this line will force all seqnames to become "chr__", which do not line up with the seqnames in my BSGenome.
This should be an option so as to allow for numeric non-"chr" prefixed seqnames when there are other non-MT non-numeric seqnames in the VCF.
In
formatVcfOutputthere is a line that adds "chr" to all chromosome names if there are any non-MT chromosomes without a "chr" prefix:https://github.com/Simon-Coetzee/motifBreakR/blob/098eeb8dfcf70b89ede1447814b2a6735cd2885e/R/locus.from.rsid.R#L132-L135
If I have a genome with numeric chromosomes, then other non-MT scaffolds that aren't numeric, this line will force all seqnames to become "chr__", which do not line up with the seqnames in my BSGenome.
This should be an option so as to allow for numeric non-"chr" prefixed seqnames when there are other non-MT non-numeric seqnames in the VCF.