@@ -122,6 +122,8 @@ combineList <- function(x, ..., BACKEND = NULL) {

     stopifnot(isTRUE(all(x_has_same_parameters)))

     # Check if all inputs have the same set of loci

     x_rowRanges <- lapply(x, rowRanges)

+    # TODO: Check if all loci are identical()/all.equal(). This is must faster

+    #       that doing all these reduce()-ing intersect()-ing

     ans_rowRanges <- Reduce(

         f = function(x, y) {

             reduce(c(x, y), drop.empty.ranges = TRUE, min.gapwidth = 0L)

@@ -215,5 +217,6 @@ combineList <- function(x, ..., BACKEND = NULL) {

         assays = ans_assays,

         rowRanges = ans_rowRanges,

         colData = ans_colData)

+    # TODO: Avoid validity check.

     .BSseq(se, parameters = ans_parameters, trans = ans_trans)

 }

@@ -360,6 +360,9 @@

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

+# TODO: If you have N cores available, are you better off using

+#       bpworkers() = N in the BPPARAM or nThread = N and use

+#       data.table::fread()? Or something in between?

 # 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

@@ -567,8 +570,9 @@ read.bismark <- function(files,

 # TODO: Add function like minfi::read.metharray.sheet()?

 # TODO: Should BACKEND really be an argument of read.bismark(); see related

 #       issue on minfi repo https://github.com/hansenlab/minfi/issues/140

-# TODO: May receive warning "In read_tokens_(data, tokenizer, col_specs, col_names,  ... : length of NULL cannot be changed". This is fixed in devel version of

-#       readr (https://github.com/tidyverse/readr/issues/833)

+# TODO: May receive warning "In read_tokens_(data, tokenizer, col_specs,

+#       col_names,  ... : length of NULL cannot be changed". This is fixed in

+#       devel version of readr (https://github.com/tidyverse/readr/issues/833).

 # TODO: Think about naming scheme for functions. Try to have the function that

 #       is bpapply()-ed have a similar name to its parent.

 # TODO: Document internal functions for my own sanity. Also, some may be useful