buildwindowdata2=function(
seq,
input="none",
twoBit,
winSize=500,
offset=0,
filelist,
filetype="bowtie",
extension,
cnvWinSize=100000,
cnvOffset=0,
outdir="default"
){
if(!file.exists(seq)){
stop(paste("Seq file not found,",seq,sep=" "))
}
if(input != "none" && !file.exists(input)){
stop(paste("Input file not found,",input,sep=" "))
}
if(!file.exists(twoBit)){
stop(paste("twoBit file not found,",twoBit,sep=" "))
}
if(filetype != "bowtie" && filetype != "tagAlign" && filetype != "bed"){
stop(paste("Incorrect filetype:",filetype,"[bowtie|tagAlign|bed]",sep=" "))
}
if(is.null(extension)){
stop(paste("extension was not specified"))
}
if(is.null(filelist)){
stop(paste("filelist was not specified"))
}
if(!file.exists(outdir) && outdir!="default"){
stop(paste("buildwindowdata: specified output directory to place built datafiles doesnt exist"))
if(!isDirectory(outdir)) stop("specified output directory path is not a directory")
}
if(substr(x=outdir, nchar(outdir), nchar(outdir)) !="/"){
outdir = paste(outdir, "/", sep="")
}
cReturn <- .C(
"buildWindowsfast",
as.character(seq),
as.character(input),
#as.character(align),
as.character(twoBit),
as.integer(winSize),
as.integer(offset),
as.integer(cnvWinSize),
as.integer(cnvOffset),
as.character(filetype),
as.character(filelist),
as.integer(extension),
as.character(outdir),
#as.integer(binary),
PACKAGE="zinba"
)
}
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