R/systemSamtools.R

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

###########################################################################/**
# @RdocDefault systemSamtools
#
# @title "Calls the samtools executable"
#
# \description{
#  @get "title".
# }
#
# @synopsis
#
# \arguments{
#   \item{command}{A @character string specifying the samtools command.}
#   \item{...}{Additional arguments specifying samtools command line switches.}
#   \item{.fake}{If @TRUE, the executable is not called.}
#   \item{verbose}{See @see "R.utils::Verbose".}
# }
#
# @author "HB"
#
# @keyword internal
#*/###########################################################################
setMethodS3("systemSamtools", "default", function(command, ..., .fake=FALSE, verbose=FALSE) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'command':
  command <- Arguments$getCharacter(command)

  # Arguments '...':
  args <- list(...)

  # Argument 'verbose':
  verbose <- Arguments$getVerbose(verbose)
  if (verbose) {
    pushState(verbose)
    on.exit(popState(verbose))
  }

  verbose && enter(verbose, "Calling samtools executable")

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Locate executable
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  bin <- findSamtools(verbose=less(verbose, 50))
  verbose && cat(verbose, "Executable:")
  verbose && print(verbose, bin)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Split up '...' arguments by system2() and samtools executable
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  keys <- names(args)
  if (is.null(keys)) {
    system2Args <- NULL
  } else {
    keep <- is.element(keys, names(formals(base::system2)))
    system2Args <- args[keep]
    args <- args[!keep]
  }

  verbose && cat(verbose, "Arguments passed to system2():")
  verbose && str(verbose, system2Args)

  verbose && cat(verbose, "Arguments passed to samtools:")
  args <- c(list(command), args)
  verbose && str(verbose, args)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Setup command line switches
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Automatically add dashes
  keys <- names(args)
  missing <- grep("^[^-]", keys)
  if (length(missing) > 0L) {
    invalid <- (args[missing] == "")
    if (any(invalid)) {
      throw("Detected non-valid command line switched: ", hpaste(args[missing][invalid]))
    }
    keys[missing] <- sprintf("-%s", keys[missing])
  }

  args <- paste(keys, args, sep=" ")
  args <- trim(args)
  verbose && cat(verbose, "Command line options:")
  verbose && print(verbose, args)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # System call
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  verbose && cat(verbose, "System call:")
  cmd <- sprintf("%s %s", bin, paste(args, collapse=" "))
  verbose && print(verbose, cmd)
  verbose && str(verbose, system2Args)

  verbose && enter(verbose, "system2() call")
  callArgs <- list(command=bin, args=args)
  callArgs <- c(callArgs, system2Args)
  verbose && str(verbose, callArgs)
  if (!.fake) {
    res <- do.call(base::system2, callArgs)
  } else {
    res <- "<fake run>"
  }

  verbose && exit(verbose)

  verbose && exit(verbose)

  res
}) # systemSamtools()