testing sparse input

SUwonglab · Feb 15, 2019 · 29d6712 · 29d6712
1 parent 2e18d6e
commit 29d6712
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/R/read_data.R b/R/read_data.R
@@ -124,15 +124,15 @@ getCountsMatrix <- function(bamfiles, peaks, PAIRED = FALSE,
  VERBOSE = FALSE){
  peaks.gr = peaks2GRanges(peaks)
  if(VERBOSE){
- print("beginning reading in counts\n")
+ message("beginning reading in counts\n")
  }
  if(byReadGroup){
  if(VERBOSE){
  message("getting counts by read group\n")
  message("read group tag = ", RGtag, "\n")
  }
  stopifnot(length(bamfiles) == 1)
- counts_mat = getCountsByReadGroup(bamfiles, peaks.gr, tag = RGtag, 
+ counts_mat = getCountsByReadGroup(bamfiles, peaks.gr, RGtag = RGtag, 
  tags2include);
  rownames(counts_mat) = peaks$name
  }