R/findHTSeq.R

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

findHTSeq <- function(..., command=c("htseq-count", "htseq-qa")) {
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Validate arguments
  # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  # Argument 'command':
  command <- match.arg(command)

  # Aroma-specific variable
  path <- getExternalHome("HTSEQ_HOME")

  versionPattern <- c(".*version ([0-9.]+(|p[0-9]+)).*")
  res <- findExternal(command=command, path=path, versionPattern=versionPattern, ...)

  # Update version format '0.5.4p3' to '0.5.4-3'
  if (!is.null(res)) {
    ver <- attr(res, "version")
    ver <- gsub("p", "-", ver, fixed=TRUE)
    attr(res, "version") <- ver
  }

  res
} # findHTSeq()