Adding chr to chromosome names should be an option

[stephenturner]

In formatVcfOutput there is a line that adds "chr" to all chromosome names if there are any non-MT chromosomes without a "chr" prefix:

motifBreakR/R/locus.from.rsid.R

Lines 132 to 135 in 098eeb8

	x <- x[!grepl("MT", seqnames(x))]
	if (!any(grepl("chr", seqlevels(x)))) {
	seqlevels(x) <- paste0("chr", seqlevels(x))
	}

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.