R/systemPicard.R

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

###########################################################################/**
# @RdocDefault systemPicard
#
# @title "Calls the Picard executable"
#
# \description{
#  @get "title".
# }
#
# @synopsis
#
# \arguments{
#   \item{command}{A @character string specifying the Picard command
#     (the name of the jar file without the *.jar extension).}
#   \item{...}{Additional arguments specifying Picard command line switches.}
#   \item{verbose}{See @see "R.utils::Verbose".}
# }
#
# \examples{\dontrun{
#   pathnameBAM <- "bwaData/LambdaVirusExample,bwa,is/Lambda_phage/reads_1.bam"
#   res <- systemPicard("ValidateSamFile", INPUT=pathnameBAM, stderr=FALSE)
#   ## ERROR: Read groups is empty
#   print(res)
#   ## [1] 1
#
#   res <- systemPicard("ValidateSamFile", INPUT=pathnameBAM,
#                       IGNORE="MISSING_READ_GROUP", stderr=FALSE)
#   ## "No errors found"
#   print(res)
#   ## [1] 0
# }}
#
#
# @author "HB"
#
# @keyword internal
#*/###########################################################################
setMethodS3("systemPicard", "default", function(command, ..., 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 Picard executable")

  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Locate executable
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  path <- findPicard(verbose=less(verbose, 50))
  verbose && cat(verbose, "Picard directory:")
  verbose && print(verbose, path)

  verbose && cat(verbose, "Picard command: ", command)
  filename <- sprintf("%s.jar", command)

  pathname <- file.path(path, filename)
  verbose && cat(verbose, "Pathname to Picard jar file: ", pathname)
  pathname <- Arguments$getReadablePathname(pathname)


  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Call Picard java jar
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  .fmtArg <- c(".*"="%s=%s")
  res <- systemJavaJar(pathname, ..., .fmtArg=.fmtArg, verbose=less(verbose, 5))

  verbose && exit(verbose)

  res
}) # systemPicard()