@@ -111,6 +111,7 @@ makeClusters <- function(hasGRanges, maxGap = 10^8) {

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

+# TODO: BSmooth() should warn if BSseq object contains mix of strands.

 # TODO: If BSmooth() encounteres errors, return `BPREDO`` as `metadata(BSseq)`

 #       so as not to clobber the user's BSseq object; see

 #       https://support.bioconductor.org/p/109374/#109459.

@@ -200,6 +200,7 @@ setMethod("findOverlaps", c("FWGRanges", "FWGRanges"), .findOverlaps_FWGRanges)

 # Internal functions -----------------------------------------------------------

+# TODO: Warn if x contains mix of + and * or - and * loci?

 .strandCollapse <- function(x) {

     stopifnot(is(x, "GenomicRanges"))

     if (all(strand(x) == "*")) return(x)

@@ -11,7 +11,8 @@ setMethod(

     "findCytosines",

     "BSgenome",

     function(x, context, seqlevels = seqlevels(x)) {

-        # NOTE: vmatchPattern,BSgenome-method returns a GRanges instance.

+        # NOTE: vmatchPattern,BSgenome-method returns a GRanges instance and

+        #       automatically checks both forward and reverse strands.

         gr <- vmatchPattern(

             pattern = context,

             subject = x,

@@ -29,25 +29,20 @@

     guessed_file_types

 }

-# TODO: (longterm, see "Alternatively ..." for a better idea)

-#       .readBismarkAsDT2(): exact same as .readBismarkAsDT() but

-#       uses utils::read.delim() instead of readr::read_tsv(). In brief

-#       benchmarking, readr::read_csv() is ~1.3-1.6x faster than

+# TODO: 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

+#       shell commands (where available) to pass compressed files. Will need to

+#       be careful of the interaction between BPPARAM and fread()'s nThread.

+#       Once implemented, move readr to Suggests. Finally, allow user to

+#       specify which function to use.

+# NOTE: In brief  benchmarking, readr::read_csv() is ~1.3-1.6x faster than

 #       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. When written, move

-#       readr to Suggests. Alternatively, re-write .readBismarkAsDT() using

-#       data.table::fread() for uncompressed files and utils::read.delim() for

-#       compressed files. This removes the dependency on readr, albeit it with

-#       slightly slower reading of compressed files. Could even then use

-#       data.table::fread() coupled with shell commands (where available) to

-#       pass compressed files. Ultimately, we want to use data.table beyond

-#       data.table::fread() whereas readr is only used for file input.

-# NOTE: This returns the file as a data.table. However, to do this it uses

-#       readr::read_tsv() + data.table::setDT() instead of data.table::fread()!

-#       Although the latter is faster, this uses the former because Bismark

-#       files are commonly compressed and readr::read_tsv() supports reading

-#       directly from compressed files whereas data.table::fread() does not.

+#       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.

 .readBismarkAsDT <- function(file,

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

                              check = FALSE,

@@ -482,7 +477,7 @@ read.bismark <- function(files,

         }

     } else {

         ptime1 <- proc.time()

-        if (verbose) message("[read.bismark] Using 'loci' as valid loci")

+        if (verbose) message("[read.bismark] Using 'loci' as candidate loci")

         if (strandCollapse) {

             if (verbose) {

                 message("[read.bismark] Collapsing strand of 'loci' ...")