@@ -172,7 +172,9 @@ BSseq <- function(M = NULL, Cov = NULL, coef = NULL, se.coef = NULL,

             stop("Cannot collapse when 'coef' or 'se.coef' are present.")

         }

         # NOTE: reduce() sorts the output

+        # TODO: Clarify above comment.

         unique_gr <- unique(gr)

+        # TODO: type = "equal"?

         ol <- findOverlaps(unique_gr, gr)

         gr <- unique(gr)

         idx <- as.list(ol)

@@ -1,5 +1,5 @@

 # TODO: Need to update NAMESPACE

-# TODO: Search both forward and reverse strands

+# TODO: Search both forward and reverse strands in a single search.

 # TODO: Default value of seqlevels as missing or NULL? Check what other

 #       functions with this arg use.

 findCytosines <- function(BSgenome, context = c("CG", "CA", "CC", "CT"),

@@ -578,3 +578,4 @@ read.bismark <- function(files,

 #       .cytosineReport files and don't want this behaviour (i.e. you want to

 #       retain strand) then you'll need to construct your own 'gr' and pass

 #       this to the function. Add unit tests for this behaviour.

+# TODO: Use verbose = getOption("verbose") as default.