
CHANGES IN VERSION 1.0.7
------------------------

BUG FIXES

    o Improved kmeans clustering
    

CHANGES IN VERSION 1.0.6
------------------------

BUG FIXES

    o Fixed an error which occurred if annotatePeaks was used with unifyBy.
    o sliceNT did not flip the exons on the negative strand in some situations.


CHANGES IN VERSION 1.0.5
------------------------

NEW FEATURES

    o gtf2gr transcript_id and gene_id attribute names can now be customized.

BUG FIXES

    o annotatePeaks returned an error when remove_unmatched was disabled. 
    o Increased filter accuracy of annotatePeaks when min_genelength > 0.


CHANGES IN VERSION 1.0.4
------------------------

NEW FEATURES

    o Setting psize to 'preserve' will enable macs2gr to return the original peak lengths.
    o annotatePeaks can now preserve the gene_id column if present.
    o Added an option to gtf2gr which defines the GTF feature type entry to be filtered during parsing  


CHANGES IN VERSION 1.0.3
------------------------

BUG FIXES

    o Improved type checking.


CHANGES IN VERSION 1.0.2
------------------------

BUG FIXES

    o Fixed a bug which resulted in wrong quality score cut off in parseReads().
    o annotatePeaks() did not accept input gtf files with present values


CHANGES IN VERSION 1.0.1
------------------------

BUG FIXES

    o Fixed a bug which resulted in wrong density maps of overlapping regions from sliceN.


CHANGES IN VERSION 1.0.0
------------------------

NEW FEATURES

    o Release version with several minor, mainly manual related improvements.


CHANGES IN VERSION 0.99.3
------------------------

NEW FEATURES

    o Renamed all C files. Registering now takes place in a separate file.
    
    o plotTV can now alternatively take a character vector of IDs matching 'transcript_id' in the gtf instead of a GRanges object. This is useful to plot RNA-Seq data matching without regions. 


BUG FIXES
   
    o Added PACKAGE argument to .call
    
	o readthrough_pairs argument to parseReads declared experimental.
	
	o Removed the matching RNA-Seq data set and added pasillaBamSubset as an example for RNA-Seq visualisation.
	

CHANGES IN VERSION 0.99.2
------------------------

NEW FEATURES

    o Added getter methods for all slots of DensityContainer and inherited classes for individual access. Added setter methods for spliced and ex_name
    
    o removed dc.size() and added the slot 'size' instead. Also added env and data_pointer slots to class DensityContainer
    
    o improved documentation of S4 methods with usage section
    
    o gtf2df and macs2df renamed to gtf2gr and macs2gr respectively. They are now returning a GRanges object.

	o annotatePeaks takes and returns only GRanges objects.
	
	o id2tss renamed to peak2tss and now returning an updated GRanges object 
	
	o plotTV accepts GRanges objects rather than data.frames for gtf and peaks input

BUG FIXES
   
    o Removed all direct slot accessions

    o Removed unnecessary call to dyn.load and dyn.unload in parseReads()
    

CHANGES IN VERSION 0.99.1
------------------------

NEW FEATURES

    o plotTV returns ordering to reproduce kmeans clustering

BUG FIXES

    o sliceNT did not flip the exons on the negative strand

    o Argument rowv to plotTV did not work with expression threshold remove_lowex 

    o Installation on 32bit Windows was not possible
