[BioC] Feature request in readVcf

[Martin Morgan]

On 09/22/2012 04:54 AM, Michael Lawrence wrote:
> Just in case you don't know, it is possible to work around this using the
> "info" slot of ScanVcfParam. But yes having a simple option to ignore
> unknown INFO and FORMAT fields would be convenient. The same should also
> apply to FILTER and ALT (in the case of structural variants).

unknown INFO and FORMAT fields now (v. 1.3.30) generate a warning and 
don't get parsed. Seems like FILTER and ALT don't currently get checked; 
are you looking for a warning on invalid value?

Martin

>
> Michael
>
> On Fri, Sep 21, 2012 at 10:51 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> Hi, Val.
>>
>> Is there in interest in simply ignoring unknown INFO and GENOTYPE fields
>> when parsing VCF files, perhaps by issuing a warning instead of an error?
>>   There are LOTS of malformed VCF files out there.  In some cases, they are
>> not useable, but in this case, they can be perfectly useable if these
>> unknown fields are simply ignored.
>>
>>> dat = readVcf('tmp.gatk.vcf',genome='hg19')
>> Error: scanVcf: record 22 INFO 'KGPilot123' not found
>>    path:
>> /Volumes/CCRBioinfo/projects/RosenbergImmuneStudy/staging/tmp.gatk.vcf
>>
>> Thanks,
>> Sean
>>
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>>
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