Thanks, should be resolved in 1.23.20 (devel).


On Fri, Mar 28, 2014 at 8:09 AM, Julian Gehring <julian.gehring@embl.de>wrote:

> Hi,
>
> Exporting a GRanges object to the 'bigwig' format with rtracklayer fails
> if not all seqlevels are used:
>
> #+BEGIN_SRC R
>   library(rtracklayer)
>   library(GenomicRanges)
>
>   ## example data
>   example(GRanges)
>   lg = reduce(unstrand(longGR))
>   lg$score = 1:6
>
>   ## full one works
>   export(lg, tempfile(), "bw") ## works
>
>   ## generally works if all seqlevels are used
>   lg1 = lg[c(1, 3, 5)]
>   export(lg1, tempfile(), "bw") ## works
>
>   ## subset works if all seqlevels are used
>   lg2 = lg[1:4]
>   export(lg2, tempfile(), "bw") ## fails
>
>   lg3 = keepSeqlevels(lg2, unique(as.character(seqnames(lg2))))
>   export(lg3, tempfile(), "bw") ## works
> #+END_SRC
>
> This fails with the latest bioc-devel (rtracklayer_1.23.18) and works
> with bioc-stable.
>
> A solution may be to remove unused seqlevels in the object, perhaps with
> a warning/message that not all seqlevels were exported.
>
> Best wishes
> Julian
>
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>

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