Hi Julian,
Thanks for this one. It was a bug in Rsamtools, now fixed in devel, version
1.15.27. I'll leave it to Martin/Val to OK it and push to release.
Michael
On Thu, Feb 6, 2014 at 1:46 AM, Julian Gehring <julian.gehr...@embl.de>wrote:
> Hi Michael,
>
> Thanks for the fast patching. However, going a step further and trying to
> read the VCF again fails (with VariantAnnotation_1.9.35
> ). I'm not sure if this is related to the same issue.
>
>
> #+BEGIN_SRC R
>
> library(VariantAnnotation)
> example(VRanges)
> writeVcf(vr, "out.vcf") ## works
> readVcf("out.vcf", "hg19") ## fails
>
> #+END_SRC
>
> Error in `rownames<-`(`*tmp*`, value = c("chr1", "chr2")) :
> invalid rownames length
>
> Best wishes
> Julian
>
>
>
> 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 12:35 AM, Julian Gehring <julian.gehr...@embl.de
>> >wrote:
>>
>> Hi,
>>>
>>> I just stumbled over the fact that 'writeVcf' for a 'VRanges' fails if
>>> 'sampleNames' is a factor with unused levels. Here a small example:
>>>
>>> #+BEGIN_SRC R
>>>
>>> library(VariantAnnotation)
>>> example(VRanges)
>>> writeVcf(vr, "out.vcf") ## works
>>>
>>> f = sampleNames(vr)
>>> f ## levels: a, b
>>> levels(f) = c("a", "b", "c") ## c in unused
>>> f ## levels: a, b, c
>>> sampleNames(vr) = f
>>> writeVcf(vr, "out.vcf") ## fails
>>>
>>> #+END_SRC
>>>
>>> Error in writeVcf(as(obj, "VCF"), filename, ...) :
>>> error in evaluating the argument 'obj' in selecting a method for
>>> function 'writeVcf': Error in ans[sampleToUniq] <- as.vector(v) :
>>> replacement has length zero
>>>
>>> This occurs both with the latest bioc-release and bioc-devel. I don't
>>> know what exactly is causing this, but please let me know if I can be of
>>> any help.
>>>
>>> Best wishes
>>> Julian
>>>
>>> _______________________________________________
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>
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