update getCounts

SUwonglab · Feb 10, 2019 · 51c0c72 · 51c0c72
1 parent a559e49
commit 51c0c72
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/R/read_data.R b/R/read_data.R
@@ -124,6 +124,9 @@ getCountsMatrix <- function(bamfiles, peaks, PAIRED = FALSE,
  VERBOSE = FALSE){
  peaks.gr = peaks2GRanges(peaks)
  if(byReadGroup){
+ if(VERBOSE){
+ message("getting counts by read group\n")
+ }
  bamfile = bamfiles;
  stopifnot(length(bamfile) == 1)
  counts_mat = getCountsByReadGroup(bamfile, peaks.gr, tag = RGtag,