CHANGES IN VERSION 2.1.3
-------------------------
NEW CITATION 
   * ASpli was published on Bioinformatics
   * https://doi.org/10.1093/bioinformatics/btab141

FEATURES
   * binGenome now displays a progress bar when binning.

BUG FIXES
    * gbCounts identifies correctly NA in junction's name
    * minAnchor in jCounts was hardcoded so it had no impact on analysis. It is being passed correctly now.

CHANGES IN VERSION 2.1
-------------------------

NEW FUNCTIONS AND FUNCTIONALITIES
    * New locus plot helper function .plotGenePattern.
       * plots coverage, junctions and architecture
       
FEATURES
    
    * Enhancement to the vignettes.
        * Quick start section was modify in order to use gtf and bam files provided by ASpli package
        * Add new section ASpli overview in vignette

BUG FIXES

    * binGenome function assigns correctly  bins located at the start and the end of each gene    
    * binGenome function calculates correctly  gene range overlap

CHANGES IN VERSION 1.99.3
-------------------------

NEW FUNCTIONS AND FUNCTIONALITIES

    * New parameters for gbCounts and jCounts functions: 
       * libType: to specify single end  ("SE") or paired end ("PE") library
       * strandMode: 
       - 0: strand of the pair is always *.
       - 1: strand of the pair is strand of its first alignment
       - 2: strand of the pair is strand of its last alignment.
    
CHANGES IN VERSION 1.99.1
-------------------------

NEW FUNCTIONS AND FUNCTIONALITIES
    
    * For counting: gbCounts  and jCounts. We add library type and strand-specificity parameters.
    
    * For DU estimation: DUreport.norm and DUreport.offset
    
    * For prepare DU reports: filterSignals, gbDUreport, integrateSignals, jDUreport, splicingReport and junctionsPJU
    
    * For printing reports: exportIntegratedSignals, writeJDU and writeSplicingReport
    
FUNCTIONS DEPRECATED
    
    * loadBAM: will be replaced by gbCounts. Bams files are proccesed one by one, according target object. It improves running time and memory usage
  
    * readCounts: it is replaced by  gbCounts
  
    * AsDiscover: it is replaced by jCounts
  
    * DUreport: it is replaced by gbDUreport and jDUreport
  
    * mergeBinDUAS: has no direct replacement. 
  
    * plotGenomicRegions: has not direct replacement. There are new functions for exportiing results into HTML pages.


CHANGES IN VERSION 1.5.1
-------------------------

BUG FIXES

    * readCounts supports identical gene names in different chromosomes.
    
    * Fixed default value for minAnchor argument of readCounts code, man page
      and vignette.  

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