Nothing
###
###
### VCF file open/close/valid
###
###
###
######
#
# is given variable a VCFhandle ?
#
vcf_valid <- function( vcffh )
{
if( class(vcffh) != "externalptr" ){ return( FALSE );}
if( names(attributes(vcffh)[1]) != "VCF.filename" ){ return( FALSE );}
return( TRUE );
}
######
#
# Open a VCF file
#
vcf_open <- function( filename )
{
if( ! is.character(filename) || length(filename)!=1 )
stop("vcf_open : parameter <filename> needs to be a single string!");
res = .Call("VCF_open", filename,PACKAGE="WhopGenome" )
return( res )
}
######
#
# Close a VCF file
#
vcf_close <- function( vcf_filehandle )
{
if( class(vcf_filehandle) != "externalptr" )
stop("vcf_close : parameter <vcffh> must be a VCFhandle as returned by vcf_open!");
res = .Call("VCF_close", vcf_filehandle,PACKAGE="WhopGenome" )
return( res )
}
######
#
# Open a VCF file
#
vcf_reopen <- function( vcffh )
{
if( class(vcffh) != "externalptr" )
stop("vcf_reopen : parameter <vcffh> must be a VCFhandle as returned by vcf_open!");
res = .Call("VCF_reopen", vcffh,PACKAGE="WhopGenome" )
return( res )
}
######
#
# Build a tabix index for a (already compressed) VCF file
#
vcf_buildindex <- function( filename ) .Call("VCF_buildindex", filename,PACKAGE="WhopGenome")
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