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Update TODOs

Peter Hickey authored on 14/06/2018 14:34:33
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@@ -29,7 +29,7 @@
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     guessed_file_types
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 }
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-# TODO: Choose between utils::read.delim(), readr::read_tsv(), and
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+# TODO: (long term) Choose between utils::read.delim(), readr::read_tsv(), and
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 #       data.table::fread() based on 'file'. If plain text, use fread(). If a
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 #       compressed file, use readr::read_tsv() if available, otherwise
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 #       utils::read_delim(). Longer term, combine data.table::fread() with
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@@ -41,8 +41,8 @@
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 #       utils::read.delim() when reading a gzipped file, albeit it with ~1.6-2x
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 #       more total memory allocated. Therefore, there may be times users prefer
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 #       to trade off faster speed for lower memory usage.
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-# TODO: Formalise these benchmarks as a document in the bsseq package so that
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-#       we can readily re-visit these as needed.
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+# TODO: (long term) Formalise these benchmarks as a document in the bsseq
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+#       package so that we can readily re-visit these as needed.
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 .readBismarkAsDT <- function(file,
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                              col_spec = c("all", "BSseq", "GRanges"),
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                              check = FALSE,
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@@ -348,7 +348,6 @@
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 # Exported functions -----------------------------------------------------------
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-# TODO: Support BPREDO?
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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