[Bioc-devel] ensemblVEP: 'fork' argument for 'VEPParam' should be integer

[Julian Gehring]

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