CHANGES IN VERSION 2.23.4
------------------------
OTHER CHANGES
  * gbCounts: removed the explicit calls to gc() inside the per-sample loops. They accounted for ~90% of the running time (gbCounts on the example data went from ~40 s to ~3 s).

CHANGES IN VERSION 2.23.3
------------------------
OTHER CHANGES
  * NAMESPACE: utils::data is no longer imported (conflicted with BiocGenerics::data and gave a warning when loading the package); limma is imported again, as required by its presence in Depends.
  * Rd cross-references to edgeR now include the package anchor.

CHANGES IN VERSION 2.23.2
------------------------
BUG FIXES
  * Solve errors "subscript out of bounds" in gbCounts, jDUreport and the splicing reports with limma >= 3.99, where limma::strsplit2 now splits by fixed strings instead of regular expressions. ASpli uses an internal helper (.strsplit2) with the previous behaviour.

OTHER CHANGES
  * Depends on R (>= 3.5.0), required by the serialized example objects in inst/extdata.

CHANGES IN VERSION 2.23.1
------------------------
FUNCTIONS DEFUNCT
  * The functions of the ASpli 1.x workflow, deprecated since the introduction of the new pipeline, were removed. See ?"ASpli-defunct" for a guide to migrate old scripts. Older Bioconductor releases still contain them.
  
    * DUreport, DUreportBinSplice: use gbDUreport (DUreport.norm and DUreport.offset remain available).
  
    * junctionDUreport: use jDUreport.
  
    * mergeBinDUAS and filterDU: use splicingReport, integrateSignals and filterSignals.
  
    * plotGenomicRegions: use exportSplicingReports and exportIntegratedSignals.
  
    * readCounts, loadBAM: use gbCounts. They are no longer exported (internal helpers of gbCounts).
  
    * AsDiscover: use jCounts. It is no longer exported (internal helper of jCounts).
  
    * aspliBamsExample was removed together with loadBAM.

OTHER CHANGES
  * NAMESPACE now uses explicit exports instead of exportPattern.
  * Added examples and \value sections to man pages, and the man page ASpli-defunct.
  * The example functions (aspliCountsExample, aspliASexample, aspliDUexample1/2, aspliJunctionDUexample) were broken because they read files missing in inst/extdata. They now read the objects stored in inst/extdata/aspli_example_objects.rds (result of the workflow on the example data). New: aspliSplicingReportExample and aspliIntegratedSignalsExample.
  * Runnable examples for DUreport.norm, DUreport.offset, filterSignals, plotBins, rds, subset and the accessors, using the example objects.
  * The vignette was converted from Sweave (Rnw) to R Markdown (BiocStyle::html_document), and a section "Migrating from ASpli v1" was added.
  * gbCounts: the junction counting code uses accessors (mcols, ranges, names) instead of direct access to S4 slots, and stops with an informative message (including the number of junctions found per sample) when no junctions are detected.
  * Code cleanup requested by BiocCheck: is() instead of class(x) == "...", vapply instead of sapply.
  * Removed the conflict of the imported function utils::findMatches with S4Vectors::findMatches.

CHANGES IN VERSION 2.19.1
------------------------
BUG FIXES
  * Solve a bug in getFilteringConditions.
  * Solve bug in jDUreport: better identification of start_J1, start_J2, and start_J3 columns.
  
CHANGES IN VERSION 2.11.1
------------------------
BUG FIXES
  * Solve a bug in readCounts. Undefined seqnames produced invalid junctions.orders
  * Change package mantainer

CHANGES IN VERSION 2.10.1
------------------------
BUG FIXES
   * Solves jCounts() Error in av[at] <- a[at] : NAs are not allowed in subscripted assignments bug with large junction possitions.

CHANGES IN VERSION 2.3.1
------------------------
BUG FIXES
   * Function vecMin inside .filterJunctionBySample threw an error if every element in counts vector was larger than the filter. Now works correctly using pmin instead. 

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
