#' Creates flanking interval(s) for each BED/GFF/VCF feature.
#'
#' @param i <bed/gff/vcf>
#' @param g <genome>
#' @param b Create flanking interval(s) using -b base pairs in each direction.
#' - (Integer) or (Float, e.g. 0.1) if used with -pct.
#'
#' @param l The number of base pairs that a flank should start from
#' orig. start coordinate.
#' - (Integer) or (Float, e.g. 0.1) if used with -pct.
#'
#' @param r The number of base pairs that a flank should end from
#' orig. end coordinate.
#' - (Integer) or (Float, e.g. 0.1) if used with -pct.
#'
#' @param s Define -l and -r based on strand.
#' E.g. if used, -l 500 for a negative-stranded feature,
#' it will start the flank 500 bp downstream. Default = false.
#'
#' @param pct Define -l and -r as a fraction of the feature's length.
#' E.g. if used on a 1000bp feature, -l 0.50,
#' will add 500 bp "upstream". Default = false.
#'
#' @param header Print the header from the input file prior to results.
#'
#' @param output Output filepath instead of returning output in R.
#'
bt.flank <- function(i, g, b = NULL, l = NULL, r = NULL, s = NULL, pct = NULL, header = NULL, output = NULL)
{
# Required Inputs
i <- establishPaths(input=i, name="i", allowRobjects=TRUE)
g <- establishPaths(input=g, name="g", allowRobjects=TRUE)
options <- ""
# Options
options <- createOptions(names=c("b", "l", "r", "s", "pct", "header"), values=list(b, l, r, s, pct, header))
# 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 flank ", options, " -i ", i[[1]], " -g ", g[[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, i[[2]], g[[2]])
deleteTempFiles(temp.files)
if(is.null(output))
return(results)
}
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