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