[Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

[Obenchain, Valerie]

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?
> 
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> 
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