[Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'
On 1/9/19 8:36 AM, Kevin RUE wrote:
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?
I don't think it's related to the vcf standard but more with handling buffer overflow gracefully under different circumstances. Valerie
Best,
Kevin
On Wed, Jan 9, 2019 at 3:49 PM Obenchain, Valerie
<Valerie.Obenchain at roswellpark.org
<mailto: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>
> <mailto: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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