Error on setting `seqlevelsStyle(gal) <- "RefSeq"`

[rcastelo]

hi,

setting seqlevelsStyle() to RefSeq works for, e.g., TxDb objects, but it gives an error with GenomicAlignment objects. Here is a minimal repex:

library(GenomicAlignments)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
seqlevelsStyle(txdb) <- "RefSeq"          ## this seems to work fine
Warning message:
In (function (seqlevels, genome, new_style)  :
  cannot switch some hg38's seqlevels from UCSC to RefSeq style
head(seqnames(seqinfo(txdb)))
[1] "NC_000001.11" "NC_000002.12" "NC_000003.12" "NC_000004.12" "NC_000005.10"
[6] "NC_000006.12"

bamfile <- system.file("extdata", "ex1.bam", package="Rsamtools",mustWork=TRUE)
gal1 <- readGAlignments(bamfile)
seqlevelsStyle(gal1) <- "RefSeq"           ## this prompts an error
Error in mapSeqlevels(x_seqlevels, value, drop = FALSE) : 
  supplied seqname style "RefSeq" is not supported

I guess if it is supported for TxDb objects, it should be also supported for GenomicAlignment objects.