#' Report overlaps between a BEDPE file and a BED/GFF/VCF file.
#'
#' @param a <bedpe>
#' @param b <bed/gff/vcf>
#' @param abam The A input file is in BAM format. Output will be BAM as well. Replaces -a.
#' - Requires BAM to be grouped or sorted by query.
#'
#' @param ubam Write uncompressed BAM output. Default writes compressed BAM.
#' is to write output in BAM when using -abam.
#'
#' @param bedpe When using BAM input (-abam), write output as BEDPE. The default
#' is to write output in BAM when using -abam.
#'
#' @param ed Use BAM total edit distance (NM tag) for BEDPE score.
#' - Default for BEDPE is to use the minimum of
#' of the two mapping qualities for the pair.
#' - When -ed is used the total edit distance
#' from the two mates is reported as the score.
#'
#' @param f Minimum overlap required as fraction of A (e.g. 0.05).
#' Default is 1E-9 (effectively 1bp).
#'
#' @param s Require same strandedness when finding overlaps.
#' Default is to ignore stand.
#' Not applicable with -type inspan or -type outspan.
#'
#' @param S Require different strandedness when finding overlaps.
#' Default is to ignore stand.
#' Not applicable with -type inspan or -type outspan.
#'
#' @param type Approach to reporting overlaps between BEDPE and BED.
#' either Report overlaps if either end of A overlaps B.
#' - Default.
#' neither Report A if neither end of A overlaps B.
#' both Report overlaps if both ends of A overlap B.
#' xor Report overlaps if one and only one end of A overlaps B.
#' notboth Report overlaps if neither end or one and only one
#' end of A overlap B. That is, xor + neither.
#' ispan Report overlaps between [end1, start2] of A and B.
#' - Note: If chrom1 <> chrom2, entry is ignored.
#' ospan Report overlaps between [start1, end2] of A and B.
#' - Note: If chrom1 <> chrom2, entry is ignored.
#' notispan Report A if ispan of A doesn't overlap B.
#' - Note: If chrom1 <> chrom2, entry is ignored.
#' notospan Report A if ospan of A doesn't overlap B.
#' - Note: If chrom1 <> chrom2, entry is ignored.
#'
#' @param output Output filepath instead of returning output in R.
#'
bt.pairtobed <- function(a, b, abam = NULL, ubam = NULL, bedpe = NULL, ed = NULL, f = NULL, s = NULL, S = NULL, type = 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("abam", "ubam", "bedpe", "ed", "f", "s", "S", "type"), values=list(abam, ubam, bedpe, ed, f, s, S, type))
# 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 pairtobed ", 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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