#' 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)
}
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