#' Pool coverage from multiple samples

 #'

 #' Averages the coverage of a list of samples.

 #'
 #'

 #' @param all.data List of normals, read with \code{\link{readCoverageFile}}.

 #' @param remove.chrs Remove these chromosomes from the pool.
 #' @param w \code{numeric(length(all.data))} vector of weights. If \code{NULL},
 #' weight all samples equally.
 #' @return A \code{data.frame} with the averaged coverage over all normals.
 #' @author Markus Riester

 #' @seealso \code{\link{readCoverageFile}}

 #' @examples

 #'

 #' normal.coverage.file <- system.file("extdata", "example_normal.txt.gz",

 #'     package = "PureCN")

 #' normal2.coverage.file <- system.file("extdata", "example_normal2.txt.gz",

 #'     package = "PureCN")

 #' normal.coverage.files <- c(normal.coverage.file, normal2.coverage.file)

 #' pool <- poolCoverage(lapply(normal.coverage.files, readCoverageFile),

 #'      remove.chrs = c("chrX", "chrY"))
 #'

 #' @export poolCoverage

 poolCoverage <- function(all.data, remove.chrs=c(), w = NULL) {

     pool <- all.data[[1]]
 

     if (length(all.data) == 1) {
         return(.removeChr(pool, remove.chrs))
     }

     if (is.null(w)) {

         w <- rep(1, length(all.data))

     } else if (length(w) != length(all.data)) {
         .stopUserError("all.data and w have different lengths.")
     }
 
     pool$coverage <- 0
     pool$counts <- 0

     for (i in seq_along(all.data)) {

         pool$coverage <- pool$coverage + (w[i] * all.data[[i]]$coverage)

         pool$counts <- pool$counts + (w[i] * all.data[[i]]$counts)

     }

     pool <- .addAverageCoverage(pool)

     return(.removeChr(pool, remove.chrs))

 }

 .removeChr <- function(pool, remove.chrs = c()) {

     idx <- seqnames(pool) %in% remove.chrs
     if (sum(idx)) {
         pool[idx]$coverage <- NA
         pool[idx]$average.coverage <- NA
     }

     pool
 }