R/bt.intersect.R

In PhanstielLab/bedtoolsr: Bedtools Wrapper

#' Report overlaps between two feature files.
#' 
#' @param a <bed/gff/vcf/bam>
#' @param b <bed/gff/vcf/bam>
#' @param wa Write the original entry in A for each overlap.
#' 
#' @param wb Write the original entry in B for each overlap.
#'   - Useful for knowing _what_ A overlaps. Restricted by -f and -r.
#' 
#' @param loj Perform a "left outer join". That is, for each feature in A
#'   report each overlap with B.  If no overlaps are found, 
#'   report a NULL feature for B.
#' 
#' @param wo Write the original A and B entries plus the number of base
#'   pairs of overlap between the two features.
#'   - Overlaps restricted by -f and -r.
#'     Only A features with overlap are reported.
#' 
#' @param wao Write the original A and B entries plus the number of base
#'   pairs of overlap between the two features.
#'   - Overlapping features restricted by -f and -r.
#'     However, A features w/o overlap are also reported
#'     with a NULL B feature and overlap = 0.
#' 
#' @param u Write the original A entry _once_ if _any_ overlaps found in B.
#'   - In other words, just report the fact >=1 hit was found.
#'   - Overlaps restricted by -f and -r.
#' 
#' @param c For each entry in A, report the number of overlaps with B.
#'   - Reports 0 for A entries that have no overlap with B.
#'   - Overlaps restricted by -f, -F, -r, and -s.
#' 
#' @param C For each entry in A, separately report the number of
#'   - overlaps with each B file on a distinct line.
#'   - Reports 0 for A entries that have no overlap with B.
#'   - Overlaps restricted by -f, -F, -r, and -s.
#' 
#' @param v Only report those entries in A that have _no overlaps_ with B.
#'   - Similar to "grep -v" (an homage).
#' 
#' @param ubam Write uncompressed BAM output. Default writes compressed BAM.
#' 
#' @param s Require same strandedness.  That is, only report hits in B
#'   that overlap A on the _same_ strand.
#'   - By default, overlaps are reported without respect to strand.
#' 
#' @param S Require different strandedness.  That is, only report hits in B
#'   that overlap A on the _opposite_ strand.
#'   - By default, overlaps are reported without respect to strand.
#' 
#' @param f Minimum overlap required as a fraction of A.
#'   - Default is 1E-9 (i.e., 1bp).
#'   - FLOAT (e.g. 0.50)
#' 
#' @param F Minimum overlap required as a fraction of B.
#'   - Default is 1E-9 (i.e., 1bp).
#'   - FLOAT (e.g. 0.50)
#' 
#' @param r Require that the fraction overlap be reciprocal for A AND B.
#'   - In other words, if -f is 0.90 and -r is used, this requires
#'     that B overlap 90 percent of A and A _also_ overlaps 90 percent of B.
#' 
#' @param e Require that the minimum fraction be satisfied for A OR B.
#'   - In other words, if -e is used with -f 0.90 and -F 0.10 this requires
#'     that either 90 percent of A is covered OR 10 percent of  B is covered.
#'     Without -e, both fractions would have to be satisfied.
#' 
#' @param split Treat "split" BAM or BED12 entries as distinct BED intervals.
#' 
#' @param g Provide a genome file to enforce consistent chromosome sort order
#'   across input files. Only applies when used with -sorted option.
#' 
#' @param nonamecheck For sorted data, don't throw an error if the file has different naming conventions
#'     for the same chromosome. ex. "chr1" vs "chr01".
#' 
#' @param sorted Use the "chromsweep" algorithm for sorted (-k1,1 -k2,2n) input.
#' 
#' @param names When using multiple databases, provide an alias for each that
#'   will appear instead of a fileId when also printing the DB record.
#' 
#' @param filenames When using multiple databases, show each complete filename
#'     instead of a fileId when also printing the DB record.
#' 
#' @param sortout When using multiple databases, sort the output DB hits
#'     for each record.
#' 
#' @param bed If using BAM input, write output as BED.
#' 
#' @param header Print the header from the A file prior to results.
#' 
#' @param nobuf Disable buffered output. Using this option will cause each line
#'   of output to be printed as it is generated, rather than saved
#'   in a buffer. This will make printing large output files 
#'   noticeably slower, but can be useful in conjunction with
#'   other software tools and scripts that need to process one
#'   line of bedtools output at a time.
#' 
#' @param iobuf Specify amount of memory to use for input buffer.
#'   Takes an integer argument. Optional suffixes K/M/G supported.
#'   Note: currently has no effect with compressed files.
#' 
#' @param output Output filepath instead of returning output in R.
#' 
bt.intersect <- function(a, b, wa = NULL, wb = NULL, loj = NULL, wo = NULL, wao = NULL, u = NULL, c = NULL, C = NULL, v = NULL, ubam = NULL, s = NULL, S = NULL, f = NULL, F = NULL, r = NULL, e = NULL, split = NULL, g = NULL, nonamecheck = NULL, sorted = NULL, names = NULL, filenames = NULL, sortout = NULL, bed = NULL, header = NULL, nobuf = NULL, iobuf = 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("wa", "wb", "loj", "wo", "wao", "u", "c", "C", "v", "ubam", "s", "S", "f", "F", "r", "e", "split", "g", "nonamecheck", "sorted", "names", "filenames", "sortout", "bed", "header", "nobuf", "iobuf"), values=list(wa, wb, loj, wo, wao, u, c, C, v, ubam, s, S, f, F, r, e, split, g, nonamecheck, sorted, names, filenames, sortout, bed, header, nobuf, iobuf))

	# 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 intersect ", 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)
}