To query for annotations of genes to human chromosomes with, e.g.,
org.Hs.eg.db, we use strings from cn <- as.character(1:22, "X", "Y", "M")
to refer to chromosomes

For annotations of SNPs to chromosomes, we use, in most cases, following
dbSNP, paste("ch", cn, sep=""), but for at least one release, put "chr" for
"ch".

In many annotation files derived from UCSC, the prefix "chr" is used; this
is true IIRC for the Hsapiens.BSgenome sequence packages.

What would it take to get all our annotation packages to respond correctly
when "chr" is the prefix, in a backwards compatible way?  It seems to me
that AnnotationDbi and the various getSNPlocs functions could be modified
to allow this without major headaches, but perhaps there are other concerns.

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