CHANGES IN VERSION 1.14.0
-------------------------

NEW FEATURES

    o The map generic and RangesMapping class for mapping ranges
      between sequences according to some alignment. Some useful
      methods are implemented in GenomicRanges.

    o The Hits class has experimental support for basic set
      operations, including setdiff, union and intersect.

    o Added a number of data manipulation functions and methods,
      including mstack, multisplit, rename, unsplit for Vector.

    o Added compare() generic for generalized range-wise comparison of 2
      range-based objects.

    o Added OverlapEncodings class and encodeOverlaps() generic for dealing
      with "overlap encodings".

    o subsetByOverlaps() should now work again on an RleViews object.

    o DataFrame now supports storing an array (like a matrix) in a column.

    o Added as.matrix,DataFrame method.

    o Added merge,DataTable,DataTable method.

    o Added disjointBins,RangesList method.

    o Added ranges,Rle and ranges,RleList methods.

    o Added which.max,Rle method.

    o Added drop,AtomicList method.

    o Added tofactor() wrapper around togroup().

    o Added coercions from vector to any AtomicList subtype (compressed and
      uncompressed).

    o Added AtomicList to Character/Numeric/Logical/Integer/Raw/ComplexList
      coercions.

    o Added revElements() for reversing individual elements of a List object.

SIGNIFICANT USER-VISIBLE CHANGES

    o RangesMatching has been renamed to Hits and extends Vector, so
      that it supports element metadata and other features. 

    o RangesMatchingList has been renamed to HitsList.

    o The 2 columns of the matrix returned by the "as.matrix" method for Hits
      objects are now named queryHits/subjectHits instead of query/subject, for
      consistency with the queryHits() and subjectHits() getters.

    o queryLength()/subjectLength() are recommended alternatives to dim,Hits.

    o breakInChunks() returns a PartitioningByWidth object.

    o The 'weight' arg in "coverage" methods for IRanges, Views and
      MaskCollection objects now can also be a single string naming a column
      in elementMetadata(x).

    o "countOverlaps" methods now propagate the names of the query.

DEPRECATED AND DEFUNCT

    o matchMatrix,Hits is deprecated.

    o Moved the following deprecated features to defunct status:
      - use of as.data.frame() or as( , "data.frame") on an AtomicList object;
      - all coercion methods from AtomicList to atomic vectors;
      - subsetting an IRanges by Ranges;
      - subsetting a RangesList or RangedData by RangesList.

BUG FIXES

    o within,RangedData/List now support replacing columns

    o aggregate() override no longer breaks on . ~ x formulas

    o "[", "c", "rep.int" and "seqselect" methods for Rle objects are now
      safer and will raise an error if the object to be returned has a
      length > .Machine$integer.max 

    o Avoid blowing up memory by not expanding 'logical' Rle's into logical
      vectors internally in "slice" method for RleList objects.


CHANGES IN VERSION 1.12.0
-------------------------

NEW FEATURES

    o Add "relist" method that works on a List skeleton.

    o Add XDoubleViews class with support of most of the functionalities
      available for XIntegerViews.

    o c() now works on XInteger and XDouble objects (in addition to XRaw
      objects).

    o Add min, max, mean, sum, which.min, which.max methods as synonyms for
      the view* functions.

SIGNIFICANT USER-VISIBLE CHANGES

    o Views and RleViewsList classes don't derive from IRanges and IRangesList
      classes anymore.

    o When used on a List or a list, togroup() now returns an integer vector
      (instead of a factor) for consistency with what it does on other
      objects (e.g. on a Partitioning object).

    o Move compact() generic from Biostrings to IRanges.

    o Drop deprecated 'multiple' argument from "findOverlaps" methods.

    o Drop deprecated 'start' and 'symmetric' arguments from "resize" method
      for Ranges objects.

DEPRECATED AND DEFUNCT

   o Using as.data.frame() and or as( , "data.frame") on an AtomicList
     object is deprecated.

   o Deprecate all coercion methods from AtomicList to atomic vectors.
     Those methods were unlisting the object, which can still be done with
     unlist().

   o Deprecate the Binning class.

   o Remove defunct overlap() and countOverlap().

BUG FIXES

   o togroup() on a List or a list does not look at the names anymore to infer
     the grouping, only at the shape of the list-like object.

   o Fix 'relist(IRanges(), IRangesList())'.

   o Fix 'rep.int(Rle(), integer(0))'.

   o Fix some long-standing issues with the XIntegerViews code (better
     handling of "out of limits" or empty views, overflows, NAs).

