[BioC] DNAStringSet_translate error in predictCoding()

[Valerie Obenchain]

Is your alt allele a DNAStringSetList or CharacterList? I am curious 
because predictCoding() should have thrown a warning along the lines of

'alt(query) must be a DNAStringSetList'

if you had a CharacterList. Otherwise this may be a bug. Can you provide 
a small reproducible example?

Valerie


On 10/31/12 21:08, Valerie Obenchain wrote:
> Hi Rebecca,
>
> It looks like your ALT variable may contain structural variants. When 
> structural variants are present in a vcf file, readVcf() will convert 
> this to a CharacterList instead of a DNAStringSetList.  Try,
>
> alt(vcf)
>
> and see if you have a DNAStringSetList. If instead you have a 
> CharacterList, see this thread for how you can subset the vcf on 
> non-structural variants.
>
> https://stat.ethz.ch/pipermail/bioconductor/2012-October/048370.html
>
> Valerie
>
>
> On 10/31/12 16:44, sun wrote:
>> Hi all,
>>
>> I got an error when I used predictCoding() in VariantAnnotation package.
>>
>>> coding<- predictCoding(vcf, txdb, injected_Arabi)
>> Error in .Call2("DNAStringSet_translate", x, DNA_BASE_CODES, lkup,
>> skipcode,  :
>>    in 'x[[24606]]': not a base at pos 3
>>
>> How can I get the value of x[[24606]]? Any suggestion for the debugging?
>>
>> Thanks,
>>
>> Rebecca
>>
>>     [[alternative HTML version deleted]]
>>
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