CHANGES IN VERSION 1.3.12
-------------------------

FEATURES

    * Events named previously as 'as' are now names 'Undefined AS' for the sake 
      of clarity.  
      
    * Enhancement to the vignettes.

BUG FIXES

    * Added verbose and filterWithContrasted arguments to DUreport method.


CHANGES IN VERSION 1.3.11
-------------------------

FEATURES

    * Change the assigning of some 'ES*' events to 'as' events.

    * Added verbose option of DUreportBinSplice method

    * junctionDUReport methods changed to junctionDUreport to be consistent with
      other methods names.

BUG FIXES

    * Many corrections in the vignette and man pages.

    * ZNF410_E013.gr.pdf file in vignettes/images was changed to 
      ZNF410_E013_gr.pdf to be correctly used in the latex code.  


CHANGES IN VERSION 1.3.10
-------------------------

DOCUMENTATION

    * Vignette is updated to reflect changes in objects, methods and functions.
      Minor revisions are still required. 

BUG FIXES

    * PlotGenomicRegions now can make plots from unmerged bams correctly.

CHANGES IN VERSION 1.3.9
------------------------

BUG FIXES

    * plotBins function now shows x-tick labels correctly.    


CHANGES IN VERSION 1.3.8
------------------------

FEATURES

    * PlotGenomicRegions do not requires an ASpliCounts object


CHANGES IN VERSION 1.3.8
------------------------

BUG FIXES

    * AsDiscover and DUreport can handle conditions with one samples. Results 
      should be taken with care, but ASpli doesn't break.

    
CHANGES IN VERSION 1.3.7
------------------------

FEATURES

    * Added functions to filter elements in ASpliCounts objects by read counts
      and read density.


CHANGES IN VERSION 1.3.6
------------------------

FEATURES

    * geneMode is the default mode of offset estimation.

CHANGES IN VERSION 1.2.1 / 1.3.1
------------------------

BUG FIXES

    * AsDiscover() no longer contains mixed row data for some IR and IR* bins in
      irPIR table. 

    * DUReport() calculates correctly junction ratio for junctions sharing their
      end in junction.counts table.
      
    * DUReport() no longer fails when there are no junctions that share their 
      start or end.
      
    * reacCounts() requires an explicit targets argument, instead of taking it 
      from the global environment (in which may not exist with that name).  

      
CHANGES IN VERSION 1.1.0
------------------------

NEW FEATURES

    * New ASpli_binGenome.log file. It reports the number of features being processed
      
CHANGES IN VERSION 0.98
-------------------------

NEW FEATURES
    
    * Multiple bins are reclassified using annotated junctions