Hi Herve,
The performance of seqlevelStyle when the genome of a GRanges object has been
set, still seems strange to me.
Here is some example code I ran in the Bioconductor:devel docker:
gr <- GRanges(rep(c("chr2", "chr3", "chrM"), 2), IRanges(1:6, 10))
genome(gr) <- "hg19"
seqlevelsStyle(gr) <-
Hi Robert,
Yes seqlevelsStyle's new behavior is slightly different and less
forgiving. The thing is that it will generally reveal dormant issues
which is not such a bad thing after all.
Note that it doesn't seem completely straightforward to retrieve the
reference genome/assembly directly
hi Hervé,
thank you very much for your clarifications, but this behavior is
different in release and has been different until now, this is BioC 3.11:
library(VariantAnnotation)
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
seqlevels(vcf)
Hi Robert,
The VCF file uses "22" for the chromosome name which is the name used by
NCBI. So explicitly specifying "hg19" in the readVcf() call is like
saying that this chromosome name is a UCSC name which is why
seqlevelsStyle() gets confused later.
If you specify the name of the NCBI
hi,
it looks like either VariantAnnotation::readVcf() or something in the
CollapsedVCF class broke in devel with respect to reading and setting
sequence styles:
library(VariantAnnotation)
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
vcf <- readVcf(fl, "hg19")
