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

NEW FEATURES

    o Add strandMode() getter and setter for GAlignmentPairs objects in
      response to the following post:

        https://support.bioconductor.org/p/65844/

      See ?strandMode for more information.

    o The readGAlignment*() functions now allow repeated seqnames in the BAM
      header.

    o Add "coverage" method for GAlignmentsList objects.

    o The strand setter now works on a GAlignmentsList object in a restricted
      way (only strand(x) <- "+" or "-" or "*" is supported).

SIGNIFICANT USER-LEVEL CHANGES

    o summarizeOverlaps() now returns a RangedSummarizedExperiment object
      (defined in the new SummarizedExperiment package) instead of an "old"
      SummarizedExperiment object (defined in the GenomicRanges package).

    o Slightly modify the behavior of junctions() on a GAlignmentPairs object
      so that the returned ranges now have the "real strand" set on them.
      See ?junctions and the documentation of the 'real.strand' argument in
      the man page of GAlignmentPairs objects for more information.

    o Add 'real.strand' argument to first() and last() getters for
      GAlignmentPairs objects.

DEPRECATED AND DEFUNCT

    o Deprecate left() and right() getters and strand() setter for
      GAlignmentPairs objects.

    o Deprecate 'invert.strand' argument of first() and last() getters for
      GAlignmentPairs objects.

    o Deprecate 'order.as.in.query' argument of "grglist" method for
      GAlignmentPairs objects.

    o Deprecate 'order.as.in.query' argument in "rglist" method for
      GAlignmentsList objects (this concept is not defined for these objects
      in general and the argument was ignored anyway).

    o After being deprecated in BioC 3.1, the "mapCoords" and "pmapCoords"
      methods are now defunct. mapToAlignments() should be used instead.

    o After being deprecated in BioC 3.1, the readGAlignment*FromBam()
      functions are now defunct. Everybody says "Let's all use the
      readGAlignment*() functions instead! (no FromBam suffix). Yeah!"

BUG FIXES

    o Various fixes to grglist/granges/rglist/ranges methods for
      GAlignmentsList objects:
      - Respect cigar information (as claimed in man page).
      - Restore 'drop.D.ranges' argument in "grglist" method (mistakenly got
        deprecated at the beginning of BioC 3.2 devel cycle).
      - The 'drop.D.ranges' argument in "rglist" method now works (was
        ignored).
      - Handle empty list elements.


CHANGES IN VERSION 1.4.0
------------------------

NEW FEATURES

    o All "findOverlaps" methods now support 'select' equal "last" or
      "arbitrary" (in addition to "all" and "first").

SIGNIFICANT USER-LEVEL CHANGES

    o Add mapToAlignments(), pmapToAlignments(), mapFromAlignments(), and
      pmapFromAlignments() as replacements for the "mapCoords" and "pmapCoords"
      methods for GAlignments objects.

    o Clarify use of 'fragments' in summarizeOverlaps() man page.

    o Tweak "show" method for GAlignments objects to display a shorter
      version of long CIGARs.

    o Add checks and more helpful error message for summarizeOverlaps() when
      "file does not exist"

DEPRECATED AND DEFUNCT

    o Deprecated readGAlignment*FromBam() functions in favor of 
      readGAlignments(), readGAlignmentPairs(), readGAlignmentsList() and
      readGappedReads().

    o Deprecated "mapCoords" and "pmapCoords" methods.

    o Removed Lngap(), Rngap(), introns(), and
      makeGAlignmentsListFromFeatureFragments() functions, and "ngap", "map",
      "pmap", and "splitAsListReturnedClass" methods (were defunct in
      GenomicAlignments 1.2.0).

BUG FIXES

    o Fix off-by-one error when processing 'S' in query_locs_to_ref_locs().


CHANGES IN VERSION 1.2.0
------------------------

NEW FEATURES

    o Add 'preprocess.reads' argument to "summarizeOverlaps" methods.

    o Add alphabetFrequencyFromBam().

SIGNIFICANT USER-LEVEL CHANGES

    o Export GappedReads() constructor.

    o coverage,Bamfile-method now returns empty RleList rather than NULL 

    o Add "mapCoords" and "pmapCoords" methods.

    o Defunct "map" and "pmap" methods (skip deprecation).

BUG FIXES

    o Bug fix in flipQuery().

    o Fix issue with "show" method for GAlignments and GAlignmentPairs objects
      when 'showHeadLines' global option is set to Inf.


CHANGES IN VERSION 1.0.0
------------------------

The first version of GenomicAlignments was included in Bioconductor 2.14. 
The package was created from existing code in IRanges, ShortRead, 
Rsamtools and GenomicRanges. 

NEW FEATURES

    o coverage,BamFile-method uses \code{yieldSize} to iterate through 
      large files

    o coverage,character-method calculates coverage from a BAM file

