Nothing
pileupDouble <- function(start, fragLength, dir,readLength, weight=1)
{
# The c code assume that readlength, fraglength and dir are specified for all reads
nbReads <- length(start)
# Recycle values for all reads in case a unique value has been provided (can be optimised, see martin and simon method)
if(length(fragLength)==1) fragLength <- rep(fragLength, nbReads)
if(length(dir)==1) dir <- rep(dir, nbReads)
if(length(readLength)==1) readLength <- rep(readLength, nbReads)
if(length(weight)==1) weight <- rep(weight, nbReads)
dir <- factor(dir, levels=c("+", "-"))
# drop non-standard values for strand direction
nonStandard <- is.na(dir)
if(any(nonStandard))
{
warning("Some undefined strand (dir) values were ignored...")
start <- start[!nonStandard]
fragLength <- fragLength[!nonStandard]
dir <- dir[!nonStandard]
readLength <- readLength[!nonStandard]
weight <- weight[!nonStandard]
}
stopifnot((length(start)==nbReads), (length(fragLength)==nbReads), (length(dir)==nbReads), (length(readLength)==nbReads), (length(weight)==nbReads))
# Compute the max coordinate possible (theoretical) in order to create in mem the resulting vector of double
maxCoord <- max(start)+max(c(max(fragLength), max(readLength)))
functionReturn <- .C("C_pileupDouble", as.integer(start), as.integer(fragLength), as.integer(dir), as.integer(readLength), as.double(weight), as.integer(nbReads), as.integer(maxCoord), res=double(maxCoord))
return(functionReturn$res)
}
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