basealigncount=function(inputfile,outputfile,twoBitFile,extension=NULL,filetype="bowtie", binary=0){
library(R.utils)
if(!file.exists(inputfile)){
stop(paste("Input file not found,",inputfile,sep=" "))
}else{
inputfile=getAbsolutePath(inputfile)
}
if(!file.exists(twoBitFile)){
stop(paste("twoBit file not found,",twoBitFile,sep=" "))
}
if(filetype != "bowtie" && filetype != "tagAlign" && filetype != "bed"){
stop(paste("Incorrect filetype:",filetype,"[bowtie|tagAlign|bed]",sep=" "))
}
if(is.null(extension)){
stop(paste("Need to specify an extension length",,sep=" "))
}
#if(is.null(getParent(outputfile))){
#
#}else if(!file.exists(getParent(outputfile))){
# stop("Directory where output is being sent doesn't exist")
#}else{
# outputfile=getAbsolutePath(outputfile)
#}
cReturn <- .C("baseAlignCounts",as.character(inputfile), as.character(outputfile), as.character(twoBitFile),as.integer(extension),as.character(filetype),as.integer(binary), PACKAGE="zinba")
if(binary==1){
library(R.utils)
cat("Because binary option is selected, appending '.bin.gz' to output path.\n")
newpath=paste(outputfile, ".bin.gz", sep="")
tar(tarfile=newpath, files=dir(path=getParent(outputfile), pattern=paste(outputfile,"_", sep="")), compression="gzip")
cat("Compressed binary basecount file can be found at", newpath, "\n")
}
}
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