Changes in version 2.11.1                        

BUG FIXES

    o   Solve bug in readCounts. Undefined seqnames produced invalid junctions.orders

    o   Change package mantainer

                       Changes in version 2.10.1                        

BUG FIXES

    o   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

    o   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 

    o   ASpli was published on Bioinformatics

    o   https://doi.org/10.1093/bioinformatics/btab141

FEATURES

    o   binGenome now displays a progress bar when binning.

BUG FIXES

    o   gbCounts identifies correctly NA in junction's name

    o   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

    o   New locus plot helper function .plotGenePattern.

    o   plots coverage, junctions and architecture

FEATURES

    o   Enhancement to the vignettes.

    o   Quick start section was modify in order to use gtf and bam files provided by ASpli package

    o   Add new section ASpli overview in vignette

BUG FIXES

    o   binGenome function assigns correctly  bins located at the start and the end of each gene    

    o   binGenome function calculates correctly  gene range overlap

                       Changes in version 1.99.3                        

NEW FUNCTIONS AND FUNCTIONALITIES

    o   New parameters for gbCounts and jCounts functions: 

    o   libType: to specify single end  ("SE") or paired end ("PE") library

    o   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

    o   For counting: gbCounts  and jCounts. We add library type and strand-specificity parameters.

    o   For DU estimation: DUreport.norm and DUreport.offset

    o   For prepare DU reports: filterSignals, gbDUreport, integrateSignals, jDUreport, splicingReport and junctionsPJU

    o   For printing reports: exportIntegratedSignals, writeJDU and writeSplicingReport

FUNCTIONS DEPRECATED

    o   loadBAM: will be replaced by gbCounts. Bams files are proccesed one by one, according target object. It improves running time and memory usage

    o   readCounts: it is replaced by  gbCounts

    o   AsDiscover: it is replaced by jCounts

    o   DUreport: it is replaced by gbDUreport and jDUreport

    o   mergeBinDUAS: has no direct replacement. 

    o   plotGenomicRegions: has not direct replacement. There are new functions for exportiing results into HTML pages.

                        Changes in version 1.5.1                        

BUG FIXES

    o   readCounts supports identical gene names in different chromosomes.

    o   Fixed default value for minAnchor argument of readCounts code, man page
	and vignette.  

                       Changes in version 1.3.12                        

FEATURES

    o   Events named previously as 'as' are now names 'Undefined AS' for the sake 
	of clarity.  

    o   Enhancement to the vignettes.

BUG FIXES

    o   Added verbose and filterWithContrasted arguments to DUreport method.

                       Changes in version 1.3.11                        

FEATURES

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

    o   Added verbose option of DUreportBinSplice method

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

BUG FIXES

    o   Many corrections in the vignette and man pages.

    o   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

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

BUG FIXES

    o   PlotGenomicRegions now can make plots from unmerged bams correctly.

                        Changes in version 1.3.9                        

BUG FIXES

    o   plotBins function now shows x-tick labels correctly.    

                        Changes in version 1.3.8                        

FEATURES

    o   PlotGenomicRegions do not requires an ASpliCounts object

BUG FIXES

    o   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

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

                        Changes in version 1.3.6                        

FEATURES

    o   geneMode is the default mode of offset estimation.

                        Changes in version 1.2.1                        

BUG FIXES

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

    o   DUReport() calculates correctly junction ratio for junctions sharing their
	end in junction.counts table.

    o   DUReport() no longer fails when there are no junctions that share their 
	start or end.

    o   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

    o   New ASpli_binGenome.log file. It reports the number of features being processed

                        Changes in version 0.98                         

NEW FEATURES

    o   Multiple bins are reclassified using annotated junctions