#' Report overlaps between two paired-end BED files (BEDPE).
#'
#' @param a <BEDPE>
#' @param b <BEDPE>
#' @param f Minimum overlap required as fraction of A (e.g. 0.05).
#' Default is 1E-9 (effectively 1bp).
#'
#' @param type Approach to reporting overlaps between A and B.
#' neither Report overlaps if neither end of A overlaps B.
#' either Report overlaps if either ends of A overlap B.
#' both Report overlaps if both ends of A overlap B.
#' notboth Report overlaps if one or neither of A's overlap B.
#' - Default = both.
#'
#' @param slop The amount of slop (in b.p.). to be added to each footprint of A.
#' *Note*: Slop is subtracted from start1 and start2
#' and added to end1 and end2.
#' - Default = 0.
#'
#' @param ss Add slop based to each BEDPE footprint based on strand.
#' - If strand is "+", slop is only added to the end coordinates.
#' - If strand is "-", slop is only added to the start coordinates.
#' - By default, slop is added in both directions.
#'
#' @param is Ignore strands when searching for overlaps.
#' - By default, strands are enforced.
#'
#' @param rdn Require the hits to have different names (i.e. avoid self-hits).
#' - By default, same names are allowed.
#'
#' @param output Output filepath instead of returning output in R.
#'
bt.pairtopair <- function(a, b, f = NULL, type = NULL, slop = NULL, ss = NULL, is = NULL, rdn = 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("f", "type", "slop", "ss", "is", "rdn"), values=list(f, type, slop, ss, is, rdn))
# 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 pairtopair ", 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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