@@ -301,6 +301,10 @@ setMethod("findOverlaps", c("FWGRanges", "FWGRanges"), .findOverlaps_FWGRanges)

                                                BPPARAM) {

     subverbose <- max(as.integer(verbose) - 1L, 0L)

+    # TODO: Instead of using the 'largest' file, use the largest

+    #       'cytosine report' file, which will have all loci in the

+    #       reference genome; provided all samples were aligned to the same

+    #       reference genome, this means it contains all loci.

     # TODO: Initialise using the 'largest' file (i.e. largest number of lines)?

     #       Would like to do this without reading the data into memory.

     #       Some benchmarks can be found at

@@ -577,7 +577,7 @@ read.bismark <- function(files,

 # TODO: (long term) Current implementation requires that user can load at least

 #       one sample's worth of data into memory per worker. Could instead read

 #       chunks of data, write to sink, load next chunk, etc.

-# TODO: Document that if 'gr' is NULL and any 'files' (especially the first

+# TODO: Document that if 'loci' is NULL and any 'files' (especially the first

 #       file) are .cov files, then any loci present in the .cov files will have

 #       their strand set to *. If you are mixing and matching .cov and

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