[Bioc-devel] VariantAnnotation: writeVcf fails if sample names not ordered

[Julian Gehring]

Great, thanks for fixing this.


On 02/05/2014 08:38 PM, Michael Lawrence wrote:
> Thanks, fixed in 1.9.35/1.8.11.
>
>
>
>
> On Wed, Feb 5, 2014 at 1:21 AM, Julian Gehring <julian.gehring at 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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>>
>