[Bioc-devel] VcfFile and VcfFileList

Valerie Obenchain vobencha at fhcrc.org
Wed Jul 17 18:56:22 CEST 2013

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?


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.
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list