@@ -29,7 +29,7 @@

     guessed_file_types

 }

-# TODO: Choose between utils::read.delim(), readr::read_tsv(), and

+# TODO: (long term) Choose between utils::read.delim(), readr::read_tsv(), and

 #       data.table::fread() based on 'file'. If plain text, use fread(). If a

 #       compressed file, use readr::read_tsv() if available, otherwise

 #       utils::read_delim(). Longer term, combine data.table::fread() with

@@ -41,8 +41,8 @@

 #       utils::read.delim() when reading a gzipped file, albeit it with ~1.6-2x

 #       more total memory allocated. Therefore, there may be times users prefer

 #       to trade off faster speed for lower memory usage.

-# TODO: Formalise these benchmarks as a document in the bsseq package so that

-#       we can readily re-visit these as needed.

+# TODO: (long term) Formalise these benchmarks as a document in the bsseq

+#       package so that we can readily re-visit these as needed.

 .readBismarkAsDT <- function(file,

                              col_spec = c("all", "BSseq", "GRanges"),

                              check = FALSE,

@@ -348,7 +348,6 @@

 # Exported functions -----------------------------------------------------------

-# TODO: Support BPREDO?

 # TODO: Support passing a colData so that metadata is automatically added to

 #       samples?

 # TODO: Document that `...` are used to pass filepath, chunkdim, level, etc. to