@@ -46,6 +46,7 @@ importFrom(readr, "cols", "cols_only", "col_character", "col_integer",

            "col_skip", "col_double", "col_factor", "read_tsv", "tokenizer_tsv")

 importFrom(Biostrings, "DNAString", "vmatchPattern", "reverseComplement")

 importFrom(utils, "read.delim")

+importFrom(BSgenome, "vmatchPattern")

 ##

 ## Exporting

@@ -54,6 +54,31 @@

     }

 }

+# Missing methods --------------------------------------------------------------

+

+# NOTE: Copied from minfi

+# TODO: Perhaps move this to DelayedMatrixStats?

+# TODO: DelayedArray::type() for all RealizationSink subclasses

+setMethod("type", "HDF5RealizationSink", function(x) {

+    x@type

+})

+# NOTE: Copied from minfi

+# TODO: Perhaps move this to DelayedMatrixStats?

+setMethod("type", "arrayRealizationSink", function(x) {

+    DelayedArray::type(x@result_envir$result)

+})

+# NOTE: Copied from minfi

+# TODO: Perhaps move this to DelayedMatrixStats?

+setMethod("type", "RleRealizationSink", function(x) {

+    x@type

+})

+# NOTE: Copied from minfi

+# TODO: Perhaps move this to DelayedMatrixStats?

+# TODO: dimnames() for all RealizationSink subclasses

+setMethod("dimnames", "arrayRealizationSink", function(x) {

+    dimnames(x@result_envir$result)

+})

+

 # Helper functions for setting up ArrayGrid instances --------------------------

 # NOTE: Copy of minfi:::colGrid()

@@ -218,6 +218,9 @@ setMethod("findOverlaps", c("FWGRanges", "FWGRanges"), .findOverlaps_FWGRanges)

 .readBismarkAsFWGRanges <- function(file, rmZeroCov = FALSE,

                                     strandCollapse = FALSE, sort = TRUE,

                                     verbose = FALSE) {

+    # Quieten R CMD check about 'no visible binding for global variable' -------

+    M <- U <- NULL

+

     # Read file to construct data.table of valid loci --------------------------

     if (rmZeroCov) {

         dt <- .readBismarkAsDT(

@@ -48,11 +48,16 @@

                              check = FALSE,

                              verbose = FALSE,

                              ...) {

+    # Quieten R CMD check about 'no visible binding for global variable' -------

+    M <- U <- NULL

+

+    # Construct the column spec ------------------------------------------------

+

     col_spec <- match.arg(col_spec)

     file_type <- .guessBismarkFileType(file)

     # TODO: Test for 'bismark_methylation_extractor' and 'bedGraph' formats,

     #       and error out (they're not supported).

-    stopifnot(S4Vectors:::isTRUEorFALSE(check))

+    stopifnot(isTRUEorFALSE(check))

     if (file_type == "cov") {

         col_names <- c("seqnames", "start", "end", "beta", "M", "U")

         if (col_spec == "BSseq") {

@@ -112,6 +117,9 @@

                 trinucleotide_context = col_character())

         }

     }

+

+    # Read the file ------------------------------------------------------------

+

     if (verbose) {

         message("[.readBismarkAsDT] Reading file '", file, "'")

     }

@@ -124,6 +132,9 @@

         quoted_na = FALSE,

         progress = verbose,

         ...)

+

+    # Construct the result -----------------------------------------------------

+

     x <- setDT(x)

     if (check && all(c("M", "U") %in% colnames(x))) {

         if (verbose) {

@@ -166,6 +177,10 @@

 .constructCountsFromSingleFile <- function(b, files, strandCollapse, loci,

                                            grid, M_sink, Cov_sink, sink_lock,

                                            verbose, BPPARAM) {

+

+    # Quieten R CMD check about 'no visible binding for global variable' -------

+    M <- U <- NULL

+

     # Read b-th file to construct data.table of valid loci and their counts ----

     file <- files[b]