it would be great if one could write things such as
gr <- droplevels(gr) or
gr <- gr[seqnames(gr) = foo, drop = TRUE], where
gr would be a
Search engines report that it has already been discussed at least once in the past, and no roadblock was mentioned.
My use case is that I am making coverage analysis with commands such as
GRanges(coverage(gr)) ; gr <- gr[score(gr) > 0], and it fails with the following error if the
gr object has unused seqlevels because it was filtered before.
Error in .normargSeqlengths(value, seqnames(x)) : length of supplied 'seqlengths' must equal the number of sequences