gistfile1.txt

bedtools = function(cmd, envir = parent.frame()) {
	gr = gsub("^.*@\\{(.*?)\\}.*$", "\\1", cmd)
	gr = get(gr, envir = envir)
	file = tempfile(fileext = ".bed")
	write.table(gr, file = file, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
	cmd = gsub("@\\{.*?\\}", file, cmd)
	try(tb <- read.table(pipe(cmd), stringsAsFactors = FALSE))
	file.remove(file)
	return(tb)
}