#' Calculate the relative distance distribution b/w two feature files.
#'
#' @param a <bed/gff/vcf>
#' @param b <bed/gff/vcf>
#' @param detail Report the relativedistance for each interval in A
#'
#' @param output Output filepath instead of returning output in R.
#'
bt.reldist <- function(a, b, detail = NULL, output = NULL)
{
# Required Inputs
a <- establishPaths(input=a, name="a", allowRobjects=TRUE)
b <- establishPaths(input=b, name="b", allowRobjects=TRUE)
options <- ""
# Options
options <- createOptions(names=c("detail"), values=list(detail))
# establish output file
tempfile <- tempfile("bedtoolsr", fileext=".txt")
tempfile <- gsub("\\", "/", tempfile, fixed=TRUE)
bedtools.path <- getOption("bedtools.path")
if(!is.null(bedtools.path)) bedtools.path <- paste0(bedtools.path, "/")
cmd <- paste0(bedtools.path, "bedtools reldist ", options, " -a ", a[[1]], " -b ", b[[1]], " > ", tempfile)
if(.Platform$OS.type == "windows") shell(cmd) else system(cmd)
if(!is.null(output)) {
if(file.info(tempfile)$size > 0)
file.copy(tempfile, output)
} else {
if(file.info(tempfile)$size > 0)
results <- utils::read.table(tempfile, header=FALSE, sep="\t", quote='')
else
results <- data.frame()
}
# Delete temp files
temp.files <- c(tempfile, a[[2]], b[[2]])
deleteTempFiles(temp.files)
if(is.null(output))
return(results)
}
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