CHANGES IN VERSION 0.1.0 (2016-01-18)
-------------------------------------

NEW FEATURES

    o First release

CHANGES IN VERSION 0.2.0 (2016-01-28)
-------------------------------------

NEW FEATURES

    o Added a global sampling factor to reduce the size of the total reads and
    genomic areas for fast overviews.
    o Coverages and profiles are not recalculated when only ordering (k-means or
    other) changes.
    o Exported kmeansDesign and removeData functions.
    o Added full reusability of the output list object of recoup. Upon a call
    using this object, only the required elements are recalculated according to
    the change in input parameters, saving a lot of computation time for simple
    plotting/profile ordering/binning changes.
    o Reduced binned coverage calculation time by two
    o Switched to bigmemory and biganalytics packages to handle coverage profile
    matrices.
    o Added sample subsetting when plotting. In this way, profiles are computed
    once and the user may choose what to plot later.
    o Added a simple setter and getter for easier manipulation and reusability
    of recoup objects.
    
BUG FIXES

    o Fixed problem with title and curve sizes in some plots


CHANGES IN VERSION 0.4.0 (2016-02-02)
-------------------------------------

NEW FEATURES

    o Removed bigmemory/biganalytics as storage is a trouble.
    o Added (almost) full reusability of recoup objects. Now the most serious,
    memory and time consuming calculations need to perform just once.
    o Added slicing/subsetting or recoup list object.
    o Broke the code in more collated files.
    o k-means design function is now much more flexible.
    
BUG FIXES

    o Fixed bug with colors in curve profile single-design plots.


CHANGES IN VERSION 0.99.4 (2016-04-02)
-------------------------------------

NEW FEATURES

    o Added support for BigWig files which greatly increases coverage reading
    speed.
    o Added plyr import to reduce memory footprints in some averaging 
    calculations.
    o Added another plot type which shows correlation between average coverage
    in summarized genomic regions and respective plot control parameters.
    o Plotting of confidence intervals for profile (and the newly added 
    correlation) plots (geom_ribbon) is now an option.
    o The setter function now supports mulitple argument setting at once.
    o Object slicing is now also performed on genomic position instead of only
    reference regions and samples.
    o Stopped automatic width in heatmaps and passed control to the user through
    the use of ... and also using ... for plots rendered with ggplot.
    o Moved sumStat and smooth options from binParams to plotParams as smoothing
    should be available for reusing/replotting recoup objects. sumStat remained
    in binParams to be used for region binning over e.g. gene bodies.
    o Added documentation for recoup_test_data
    o Added small BAM files for testing of the preprocessRanges()) function.
    o Updated vignettes.
    
BUG FIXES
    o Fixed bug when reading reads from bed files. GenomeInfoDb is used to fill
    the seqinfo slot of the produced GenomicRanges. Credits to Orsalia Hazapis,
    BSRC 'Alexander Fleming'.
    o Fixed bug when region is "custom" and the intervals were not of fixed 
    width. Credits to Orsalia Hazapis, BSRC 'Alexander Fleming'.
    o Fixed bug in custom heatmap ordering.
    o Fixed bug in calculation of average profiles in recoupCorrelation when
    using mean/median instead of splines.


CHANGES IN VERSION 1.1.3 (2017-04-03)
-------------------------------------

NEW FEATURES

    o Major improvements in speed and memory consumption.
    o RNA-Seq plots can now use pre-calculated ranges. This is advised for 
    these plots as on-the-fly GenomicRanges manipulations can take time. See
    details in the buildAnnotationStore function.
    o Added a function for merging runs. This is very useful in the case of 
    having to analyze many files including large regions (e.g. gene bodies
    o Chunking of large regions in now an option. Further reduces memory usage
    for large genomic regions with large BAM files.
    
BUG FIXES
    o Fixed some bugs when using external annotations and on-the-fly 
    calculations.


CHANGES IN VERSION 1.7.2 (2018-04-25)
-------------------------------------

NEW FEATURES

    o New faster annotation building system which keeps also versions. May
    break older annotation stores. A rebuild is advised.
    o More supported genomes
BUG FIXES
    o Fixed a bug resulting in profile bleeding when using a mask of ranges
    from a BAM file.
    

CHANGES IN VERSION 1.17.1 (2020-05-03)
-------------------------------------

NEW FEATURES

    o New annotation based on an SQLite database. Rebuild must be performed
    otherwise the application will break. Download of a ready made annotation
    is also available (see vignette).
    o More supported genomes
    o Quick, high-level profile based on RPM instead of coverage
    o Speed and code improvements
BUG FIXES
    o Fixed bug resulting in running the same operation multiple times when
    chunking was requested.
