#' Take sample of input file(s) using reservoir sampling algorithm.
#'
#' @param i <bed/gff/vcf/bam>
#' @param n The number of records to generate.
#' - Default = 1,000,000.
#' - (INTEGER)
#'
#' @param seed Supply an integer seed for the shuffling.
#' - By default, the seed is chosen automatically.
#' - (INTEGER)
#'
#' @param ubam Write uncompressed BAM output. Default writes compressed BAM.
#'
#' @param s Require same strandedness. That is, only give records
#' that have the same strand. Use '-s forward' or '-s reverse'
#' for forward or reverse strand records, respectively.
#' - By default, records are reported without respect to strand.
#'
#' @param header Print the header from the A file prior to results.
#'
#' @param bed If using BAM input, write output as BED.
#'
#' @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.sample <- function(i, n = NULL, seed = NULL, ubam = NULL, s = NULL, header = NULL, bed = NULL, nobuf = NULL, iobuf = NULL, output = NULL)
{
# Required Inputs
i <- establishPaths(input=i, name="i", allowRobjects=TRUE)
options <- ""
# Options
options <- createOptions(names=c("n", "seed", "ubam", "s", "header", "bed", "nobuf", "iobuf"), values=list(n, seed, ubam, s, header, bed, 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 sample ", options, " -i ", i[[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]])
deleteTempFiles(temp.files)
if(is.null(output))
return(results)
}
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