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Add TODOs

Peter Hickey authored on 28/06/2018 23:34:03
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@@ -122,6 +122,8 @@ combineList <- function(x, ..., BACKEND = NULL) {
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     stopifnot(isTRUE(all(x_has_same_parameters)))
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     # Check if all inputs have the same set of loci
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     x_rowRanges <- lapply(x, rowRanges)
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+    # TODO: Check if all loci are identical()/all.equal(). This is must faster
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+    #       that doing all these reduce()-ing intersect()-ing
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     ans_rowRanges <- Reduce(
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         f = function(x, y) {
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             reduce(c(x, y), drop.empty.ranges = TRUE, min.gapwidth = 0L)
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@@ -215,5 +217,6 @@ combineList <- function(x, ..., BACKEND = NULL) {
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         assays = ans_assays,
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         rowRanges = ans_rowRanges,
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         colData = ans_colData)
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+    # TODO: Avoid validity check.
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     .BSseq(se, parameters = ans_parameters, trans = ans_trans)
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 }
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@@ -360,6 +360,9 @@
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 # Exported functions -----------------------------------------------------------
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+# TODO: If you have N cores available, are you better off using
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+#       bpworkers() = N in the BPPARAM or nThread = N and use
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+#       data.table::fread()? Or something in between?
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 # TODO: Support passing a colData so that metadata is automatically added to
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 #       samples?
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 # TODO: Document that `...` are used to pass filepath, chunkdim, level, etc. to
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@@ -567,8 +570,9 @@ read.bismark <- function(files,
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 # TODO: Add function like minfi::read.metharray.sheet()?
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 # TODO: Should BACKEND really be an argument of read.bismark(); see related
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 #       issue on minfi repo https://github.com/hansenlab/minfi/issues/140
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-# 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
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-#       readr (https://github.com/tidyverse/readr/issues/833)
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+# TODO: May receive warning "In read_tokens_(data, tokenizer, col_specs,
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+#       col_names,  ... : length of NULL cannot be changed". This is fixed in
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+#       devel version of readr (https://github.com/tidyverse/readr/issues/833).
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 # TODO: Think about naming scheme for functions. Try to have the function that
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 #       is bpapply()-ed have a similar name to its parent.
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 # TODO: Document internal functions for my own sanity. Also, some may be useful