CHANGES IN VERSION 1.6.0
------------------------

NEW FEATURES

    o seqlevels() and seqinfo() setters have a new arg ('force', default is
      FALSE) to force dropping sequence levels currently in use.

    o Seqinfo objects now have a genome column that can be accessed with
      genome() getter/setter.

    o "pgap" method for c(x="GRanges", y="GRanges").

    o Add comparison (==, <=, duplicated, unique, etc...) and ordering
      (order, sort, rank) methods for GenomicRanges objects.

    o Add "flank" method for GRangesList objects.

    o Add "isDisjoint" and "restrict" methods for GRanges and GRangesList
      objects.

    o Add GRangesList constructor makeGRangesListFromFeatureFragments().

    o Add "names" and "names<-" methods for GappedAlignments objects.

    o Add 'ignore.strand' arg to a number of methods:
        - findOverlaps,GRangesList,RangesList
        - findOverlaps,GappedAlignments,ANY
        - findOverlaps,ANY,GappedAlignments

    o 'shift' and 'weight' arguments of "coverage" method for GenomicRanges
      objects now can be numeric vectors in addition to lists.

    o Add "c" method for GappedAlignments objects.

SIGNIFICANT USER-VISIBLE CHANGES

    o readGappedAlignments() supports 2 new arguments: (1) 'use.names' (default
      is FALSE) for using the query template names (QNAME field in a SAM/BAM
      file) to set the names of the returned object, and (2) 'param' (default
      is NULL, otherwise a ScanBamParam object) for controlling what fields and
      which records are imported. readGappedAlignments() doesn't support
      the 'which' arg anymore.

    o The names of a GRanges/GRangesList/GappedAlignments object are not
      required to be unique anymore.

    o By default, the rownames are not set anymore on the DataFrame returned
      by elementMetadata() on a GRanges/GRangesList/GappedAlignments object.

    o 'width' arg of "coverage" method for GenomicRanges objects now must be
      NULL or numeric vector (instead of NULL or list).

DEPRECATED AND DEFUNCT

    o Deprecate countGenomicOverlaps() in favor of summarizeOverlaps().

    o Deprecate grg() in favor of granges().

BUG FIXES

    o Fix bug in "pintersect" methods operating on GappedAlignments objects.