testing sparse input

SUwonglab · Feb 15, 2019 · eff769e · eff769e
1 parent 29d6712
commit eff769e
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/R/read_data.R b/R/read_data.R
@@ -77,8 +77,8 @@ getCountsByReadGroup <- function(bamfile, peaks, RGtag, tags = NULL, PAIRED = FA
  }
  counts_mat = Matrix::Matrix(0, nrow = length(peaks), 
  ncol = length(tags), sparse = TRUE)
- for(i in 1:length(RGtags)){
- tag = RGtags[i]
+ for(i in 1:length(tags)){
+ tag = tags[i]
  if(VERBOSE){
  message("Processing tag ", tag)
  }
@@ -133,7 +133,7 @@ getCountsMatrix <- function(bamfiles, peaks, PAIRED = FALSE,
  }
  stopifnot(length(bamfiles) == 1)
  counts_mat = getCountsByReadGroup(bamfiles, peaks.gr, RGtag = RGtag, 
- tags2include);
+ tags = tags2include);
  rownames(counts_mat) = peaks$name
  }
  else{