R/filterdup.R

In macs3-project/MACSr: MACS: Model-based Analysis for ChIP-Seq

#' filterdup
#'
#' @param ifile Input file(s).
#' @param gsize Effective genome size. It can be 1.0e+9 or 1000000000,
#'     or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9),
#'     'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8),
#'     Default:hs.
#' @param format Input file format.
#' @param tsize Tag size. This will override the auto detected tag
#'     size.
#' @param pvalue Pvalue cutoff for binomial distribution
#'     test. DEFAULT:1e-5.
#' @param keepduplicates It controls the behavior towards duplicate
#'     tags at the exact same location -- the same coordination and
#'     the same strand. The 'auto' option makes MACS calculate the
#'     maximum tags at the exact same location based on binomal
#'     distribution using 1e-5 as pvalue cutoff; and the 'all' option
#'     keeps every tags.  If an integer is given, at most this number
#'     of tags will be kept at the same location. Note, if you've used
#'     samtools or picard to flag reads as 'PCR/Optical duplicate' in
#'     bit 1024, MACS2 will still read them although the reads may be
#'     decided by MACS2 as duplicate later. If you plan to rely on
#'     samtools/picard/any other tool to filter duplicates, please
#'     remove those duplicate reads and save a new alignment file then
#'     ask MACS2 to keep all by '--keep-dup all'. The default is to
#'     keep one tag at the same location. Default: 1".
#' @param outputfile The output file.
#' @param outdir The output directory.
#' @param verbose Set verbose level of runtime message. 0: only show
#'     critical message, 1: show additional warning message, 2: show
#'     process information, 3: show debug messages.  DEFAULT: 2.
#' @param buffer_size Buffer size for incrementally increasing
#'     internal array size to store reads alignment information. In
#'     most cases, you don't have to change this parameter. However,
#'     if there are large number of chromosomes/contigs/scaffolds in
#'     your alignment, it's recommended to specify a smaller buffer
#'     size in order to decrease memory usage (but it will take longer
#'     time to read alignment files). Minimum memory requested for
#'     reading an alignment file is about # of CHROMOSOME *
#'     BUFFER_SIZE * 8 Bytes. DEFAULT: 100000.
#' @param dryrun When set, filterdup will only output numbers instead
#'     of writing output files, including maximum allowable
#'     duplicates, total number of reads before filtering, total
#'     number of reads after filtering, and redundant rate. Default:
#'     not set.
#' @param log Whether to capture logs.
#' @importFrom utils read.table
#' @return `macsList` object.
#' @export
#' @examples
#' eh <- ExperimentHub::ExperimentHub()
#' CHIP <- eh[["EH4558"]]
#' res <- filterdup(ifile = CHIP, outputfile = "test.bed", outdir = tempdir())
filterdup <- function(ifile, gsize = "hs", format = "AUTO",
                      tsize = NULL, pvalue = 1e-5, keepduplicates = "auto",
                      outputfile = character(), outdir = ".", verbose = 2L,
                      buffer_size = 10000, dryrun = FALSE, log = TRUE){
    if(is.character(ifile)){
        ifile <- as.list(normalizePath(ifile))
    }

    cl <- basiliskStart(env_macs)
    on.exit(basiliskStop(cl))
    res <- basiliskRun(cl, function(.namespace, outdir){
        opts <- .namespace()$Namespace(gsize = gsize,
                                       tsize = tsize,
                                       pvalue = pvalue,
                                       format = format,
                                       keepduplicates = keepduplicates,
                                       verbose = verbose,
                                       outputfile = outputfile,
                                       outdir = outdir,
                                       ifile = ifile,
                                       buffer_size = buffer_size,
                                       dryrun = dryrun)
        .filterdup <- reticulate::import("MACS3.Commands.filterdup_cmd")
        if(log){
            reticulate::py_capture_output(.filterdup$run(opts))
        }else{
            .filterdup$run(opts)
        }
    }, .namespace = .namespace, outdir = outdir)
    if(log){
        message(res)
    }
    ofile <- file.path(outdir, outputfile)
    args <- as.list(match.call())
    macsList(arguments = args, outputs = ofile, log = res)
}