Nothing
###
###
### Regions
###
###
###
#
#
#
vcf_getregion <- function( vcffh ) return( .Call("VCF_getRegion", vcffh, PACKAGE="WhopGenome" ) )
#
# set region to scan - each component is specified individually or as "chr:begin-end" string
#
vcf_setregion <- function( vcffh , tid, from=NA, to=NA )
{
if( is.na(from) || is.na(to) )
{
tid_reg = strsplit( tid, ":" )
stopifnot( length(tid_reg[[1]]) == 2 )
tid = tid_reg[[1]][1]
beg_end = strsplit( tid_reg[[1]][2] , "-" )[[1]]
from = as.integer( beg_end[1] )
to = as.integer( beg_end[2] )
}
tid = as.character( tid )
from = as.integer(from)
to = as.integer(to)
if( from <= 0 || to <= 0 || to < from ){ stop("begin-end is wrong!") }
res <- .Call("VCF_setRegion", vcffh, tid, from, to, PACKAGE="WhopGenome" )
return( res );
}
#
# scan last set region from start again
#
vcf_restartregion <- function( vcffh ) .Call("VCF_restartRegion",vcffh,PACKAGE="WhopGenome")
#
# TRUE if all lines within region have been read, FALSE if there are some left
#
vcf_eor <- function( vcffh ) .Call("VCF_eor",vcffh,PACKAGE="WhopGenome")
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