Thanks for catching this. A fix is checked in to 0.99.13.
It's great to have a tester for this package. Let me know if you have
suggestions/feedback for the user interface, how the param options are
specified etc.
Valerie
On 02/27/13 07:25, Julian Gehring wrote:
Hi,
'VEPParam' allows to set the parameters for the ensembl VEP perl
script, and the documentation of 'ensemblVEP' specifies:
"""
- fork: ‘logical’, default FALSE; enable forking
"""
However, looking at the VEP documentation
(http://www.ensembl.org/info/docs/variation/vep/vep_script.html#forking)
and the example below, it should rather accept an integer than a
logical value:
"""
library(ensemblVEP)
file <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
## works ##
vcf <- ensemblVEP(file, param=VEPParam())
## also works ##
vcf <- ensemblVEP(file, param=VEPParam(basic=c(fork=FALSE)))
## is not valid, requires a logical ##
vcf <- ensemblVEP(file, param=VEPParam(basic=c(fork=2L)))
Error in validObject(.Object) :
invalid class “VEPParam” object: 2 must be TRUE or FALSE
## does not work ##
vcf <- ensemblVEP(file, param=VEPParam(basic=c(fork=TRUE)))
Value "--species" invalid for option fork (number expected)
ERROR: Failed to parse command-line flags
Error in .io_check_exists(path(con)) : file(s) do not exist:
'/tmp/RtmpjR3p8p/file7a4f5271f65c'
"""
Best wishes
Julian
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