R/setConfiguration.R

In piotrcirocki/BCTs-finder: BCTs-finder

ConfigurationInitializer <- function() {

  thisEnv <- environment()

  me <- list(thisEnv = thisEnv, setConfiguration = function(value) {
    what <- c("rname", "pos", "qwidth", "seq", "isize", "flag", "mrnm", "mpos")

    param <- Rsamtools::ScanBamParam(what = what, flag = Rsamtools::scanBamFlag(isProperPair = F, isUnmappedQuery = FALSE, hasUnmappedMate = FALSE))

    bam <- Rsamtools::scanBam(value, param = param)

    .unlist <- function(x) {
      x1 <- x[[1L]]
      if (is.factor(x1)) {
        structure(unlist(x), class = "factor", levels = levels(x1))
      } else {
        do.call(c, x)
      }
    }
    bam <- unname(bam)  # names not useful in unlisted result
    elts <- setNames(Rsamtools::bamWhat(param), Rsamtools::bamWhat(param))
    lst <- lapply(elts, function(elt) .unlist(lapply(bam, "[[", elt)))
    #df <- do.call(base::rbind.data.frame, lst)
    # f = function(x) function(i) sapply(x, `[[`, i)
    #df <- as.data.frame(Map(f(lst), names(lst[[1]])))
    df <- as.data.frame(lst)
    df["rdir"] <- sapply(df$flag, function(x) {
      index <- "N"
      if (bitwAnd(x, 32) != 0) {
        index <- "F"
      } else if (bitwAnd(x, 16) != 0) {
        index <- "R"
      } else index <- "N"
      return(index)
    })
    mydf <- df[!df$rname == "chrM", ]
    mydf <- mydf[!mydf$mrnm == "chrM", ]

    mydf$ID <- seq.int(nrow(mydf))
    mydf <- mydf[which(mydf$rdir != "N"),]
    return(assign("myDataframe", mydf, thisEnv))
  }, getConfiguration = function() {
    return(get("myDataframe", thisEnv))
  })

  assign("this", me, envir = thisEnv)

  ## Set the name for the class
  class(me) <- append(class(me), "ConfigurationInitializer")
  return(me)
}