[Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'
Thanks for the update Valerie. Needless to say, I ran R CMD check locally yesterday, and it crashed with the same issue. Naive question, without looking into the original issue: is it purely a programming issue, or is there a chance that our (seqCAT and TVTB) VCF files need to be updated to match any kind of new standard? Best, Kevin On Wed, Jan 9, 2019 at 3:49 PM Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:
The problem is related to a change I made to handle buffer overflow: https://github.com/Bioconductor/VariantAnnotation/issues/19 This clearly doesn't work for all cases, thanks for reporting the problems with seqCAT and TVTB. I've reverted the change so your packages will build and will re-think the fix. Valerie On 1/8/19 10:45 AM, Kevin RUE wrote:
Hi all, Same kind of error for my TVTB package (
I'll run R CMD check locally ASAP to see whether I need to update TVTB
or if it's something upstream.
Best,
Kevin
On Tue, Jan 8, 2019 at 5:05 PM Obenchain, Valerie
<Valerie.Obenchain at roswellpark.org
<mailto:Valerie.Obenchain at roswellpark.org>> wrote:
Hi Erik,
There have been a few changes to VariantAnnotation lately. I'll take
a
look at seqCAT and get back to you.
Valerie
On 1/8/19 6:07 AM, Erik Fasterius wrote:
> I recently started to get a weird error when building the
vignette to my seqCAT package, related to a VCF file I use as
example data. The error itself looks like this:
>
> scanVcf: _DNAencode(): invalid DNAString input character: '1'
(byte value 49) path: (...)/seqCAT/extdata/example.vcf.gz
>
> I can also reproduce the error by a simple
`VariantAnnotation::readVCF()` call. It has worked fine until the
latest devel-updates of other Bioconductor packages, so I assumed it
was some new change that caused the error, but I cannot find
anything in the NEWS seemingly related to this. I also tried to
troubleshoot by manually inspecting my file, and it seems that the
ANN field is the culprit; I can read the VCF if I remove the
entirety of the INFO column. I cannot, however, seem to locate the
erroneous data itself.
>
> Does anybody have any idea what causes this?
>
> [[alternative HTML version deleted]]
>
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