I think there are fairly clear use cases for a VcfFile class. It's nice to
be able to dispatch on the file/path, for example in visualization tools.
Please add this when you have a chance.

Thanks,
Michael


On Wed, Jul 17, 2013 at 9:56 AM, Valerie Obenchain <vobencha@fhcrc.org>wrote:

> Hi Robert,
>
> Have you seen TabixFile and TabixFileList? Both scanVcf() and readVcf()
> have methods for TabixFile.
>
> > showMethods("readVcf")
> Function: readVcf (package VariantAnnotation)
> file="character", genome="character", param="missing"
> file="character", genome="character", param="ScanVcfParam"
> file="character", genome="missing", param="missing"
> file="TabixFile", genome="character", param="GRanges"
> file="TabixFile", genome="character", param="GRangesList"
> file="TabixFile", genome="character", param="missing"
> file="TabixFile", genome="character", param="RangedData"
> file="TabixFile", genome="character", param="RangesList"
> file="TabixFile", genome="character", param="ScanVcfParam"
>
> Does this fit your need/use case?
>
> Valerie
>
>
> On 07/17/2013 03:22 AM, Robert Castelo wrote:
>
>> hi,
>>
>> i'm interested in having classes 'VcfFile' and 'VcfFileList', analogous
>> to 'BamFile'/'BamFileList' or 'Bcf/BcfFileList,' with their
>> corresponding functionality to ease manipulating, in this case, VCF
>> files. i thought i could sort of copy&paste code from Rsamtools but the
>> existing definitions of classes and methods rely on the Rsamtools
>> internal functions '.RsamtoolsFile' and '.RsamtoolsFileList' which are
>> not exported, and thus i cannot use them.
>>
>> i might be following the wrong path, so i'd like to ask how should i
>> proceed to have this kind of functionality to handle VCF files,
>> analogous to the existing one in Rsamtools to handle BAM or BCF files.
>>
>> thanks!
>> robert.
>>
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