[Bioc-devel] GenomicRanges: Seqinfo indexing with non-existing key

[Dan Du]

Hi,

To me it sounds like what I am expecting, from a R base point of view.

x<-1:5
names(x)<-letters[1:5]
i<-'f'
x[i]

Best,
Dan

On Thu, 2014-02-27 at 13:49 +0100, Julian Gehring wrote:
> Hi,
> 
> In the current bioc-stable and bioc-devel, a 'Seqinfo' object can be
> indexed successfully with any character key, even it is non-existing:
> 
> #+BEGIN_SRC R
>   library(GenomicRanges)
>   library(BSgenome.Hsapiens.UCSC.hg19)
> 
>   si = seqinfo(BSgenome.Hsapiens.UCSC.hg19)
> 
>   ind2 = "999"
>   ind2 %in% seqnames(si) ## FALSE, no seqlevel with this name
> 
>   si[ind2] ## works, but should not
> #+END_SRC
> 
> Shouldn't this throw an error?
> 
> Best wishes
> Julian
> 
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