[Bioc-devel] VcfFile and VcfFileList

[Robert Castelo]

hi Valerie,

sounds great, and i think it will do, however, i've encountered a 
problem when trying to obtain the tabix index file, required to build 
this TabixFile object, with a toy VCF file i'm playing with:

library(Rsamtools)
indexTabix("x.vcf.gz")
Error in value[[3L]](cond) : 'seq' must be integer(1)
   file: x.vcf.gz

the message sounds to me complaining about the sequence names (?)

library(VariantAnnotation)
vcf <- readVcf("x.vcf.gz", genome="hg19")
seqnames(vcf)
factor-Rle of length 5000 with 5 runs
   Lengths:  704  993 1911 1370   22
   Values :   20   21   22    X    Y
Levels(5): 20 21 22 X Y

so could the problem be that sequence names are not integers because of 
X and Y ?

thanks!
robert.

On 7/17/13 6:56 PM, Valerie Obenchain 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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>