Thanks, fixed in 1.9.35/1.8.11.




On Wed, Feb 5, 2014 at 1:21 AM, Julian Gehring <julian.gehring@embl.de>wrote:

> Hi,
>
> I'm not sure whether this is related to the other bug.  Anyway, 'writeVcf'
> fails if the sample names of a 'VRanges' object are not sorted in ascending
> order (in the latest bioc-devel):
>
> #+BEGIN_SRC R
>   library(VariantAnnotation)
>
>   vr = VRanges(1:2, IRanges(100:101, 200:201),
>       ref = c("G", "G"), alt = c("A", "T"))
>
>   sampleNames(vr) = factor(c("1", "2"))
>   writeVcf(vr, tempfile())  ## works, also for "A"/"B", etc
>
>   sampleNames(vr) = factor(c("2", "1"))
>   writeVcf(vr, tempfile())  ## fails, also for "B"/"A", etc.
>   ## convertion to VCF itself works
>   vcf = as(vr, "VCF")
>   writeVcf(vcf, tempfile())  ## fails
> #+END_SRC
>
> with the error:
>
> Error in relist(genoMatFlat, PartitioningByEnd(genoMat)) :
>   shape of 'skeleton' is not compatible with 'NROW(flesh)'
>
> In bioc-release (VariantAnnotation_1.8.10), it fails irrespective of the
> sample name order:
>
> #+BEGIN_SRC R
>   library(VariantAnnotation)
>
>   vr = VRanges(1:2, IRanges(100:101, 200:201),
>       ref = c("G", "G"), alt = c("A", "T"))
>
>   sampleNames(vr) = factor(c("1", "2"))
>   writeVcf(vr, tempfile())  ## fails
> #+END_SRC
>
> with
>
> Error in writeVcf(as(obj, "VCF"), filename, ...) :
>   error in evaluating the argument 'obj' in selecting a method for
> function 'writeVcf': Error in listClassName("Compressed", class(x)) :
>   Could not find a 'CompressedList' subclass for values of type '
> CompressedRleListRleListCompressedAtomicListAtomicListCompre
> ssedListListVectorAnnotated'
>
>
> Please let me know if I can help.
>
> Best wishes
> Julian
>
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>

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