oops!! i was forgetting the 'format="vcf"' argument in the call to
indexTabix. it works now, sorry for the noise!
robert.
On 7/17/13 8:24 PM, Robert Castelo wrote:
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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