TODO

IRanges before the split (version 1.23.5)
-----------------------------------------

R files: 73 files

  Going to S4Vectors (29 files in total):
  X S4-utils.R
  X utils.R
  X isConstant.R        (renamed isSorted.R)
  X normarg-utils.R
  X compact_bitvector.R (deleted)
  X int-utils.R
  X str-utils.R
  X vector-utils.R      (NEW!)
  X eval-utils.R

  X Annotated-class.R
  X DataTable-API.R     (rename DataTable-class.R, put DataTable class def here)
  X DataTable-stats.R   (merge with DataTable-class.R)

  X subsetting-utils.R 
  X Vector-class.R      (there are some leftovers in IRanges/R/Vector-class.R)
  X Vector-comparison.R
  X Hits-class.R        (there are some leftovers in IRanges/R/Hits-class.R)

  X Rle-class.R         (too big! split in Rle-class.R + Rle-utils.R)
  X runstat.R           (merge with Rle-utils.R)

  X List-class.R        (split in List-class.R + List-utils.R)
  X endoapply.R         (merge with List-utils.R)
  X funprog-methods.R   (merge with List-utils.R)
  X SimpleList-class.R

  X DataFrame-class.R

    List-comparison.R   (methods for CompressedList need to stay in IRanges)

    DataFrame-utils.R
    expand-methods.R    (merge with DataFrame-utils.R)

  X FilterRules-class.R

    classNameForDisplay-methods.R (no more, has been diluted in other files)
    zzz.R

C files:

- 36 compilation units (.c files)

  Going to S4Vectors (15 files in total):
  X safe_arithm.c
  X sort_utils.c
  X hash_utils.c
  X AEbufs.c
  X SEXP_utils.c (split in SEXP_utils.c + vector_utils.c + eval_utils.c)
  X anyMissing.c
  X compact_bitvector.c (deleted)
  X int_utils.c
  X str_utils.c
  X Hits_class.c
  X Rle_class.c
  X Rle_utils.c
  X Vector_class.c (renamed List_class.c)
  X SimpleList_class.c
  X DataFrame_class.c

- 9 header files (.h files)

  None goes to S4Vectors.


Other TODO items that originated in the IRanges package
-------------------------------------------------------

o FilterRules:
  - refactor, using ShortRead filter framework (becomes FilterList)
  - support subsetting DataFrame/RangedData directly

oooooooo