
CHANGES IN VERSION 1.15.1
------------------------

BUG FIXES

    o Importing from S4Vectors instead of IRanges


CHANGES IN VERSION 1.7.4
------------------------

BUG FIXES

    o Removed import error introduced with version 1.7.2


CHANGES IN VERSION 1.7.3
------------------------

BUG FIXES

    o Minor bug fix


CHANGES IN VERSION 1.7.2
------------------------

NEW FEATURES

    o annotatePeaks now assigns a gene to the peak center instead of the peak limits
    o annotatePeaks takes the new argument 'reference' to enable alternative peak to gene body associations


CHANGES IN VERSION 1.7.1
------------------------

BUG FIXES

    o Minor correction to avoid warning messages issued after GRanges to data.frame conversion


CHANGES IN VERSION 1.5.9
------------------------

BUG FIXES

    o Use of mcols in favor of values to access meta data in GRanges objects


CHANGES IN VERSION 1.5.8
------------------------

BUG FIXES

    o Minor bug fix in annotatePeaks to accommodate recent changes in GRanges


CHANGES IN VERSION 1.5.7
------------------------

BUG FIXES

    o Minor bug fix in annotatePeaks


CHANGES IN VERSION 1.5.6
------------------------

BUG FIXES

    o Minor bug fix


CHANGES IN VERSION 1.5.5
------------------------

BUG FIXES

    o Speed improvement and improved accuracy of annotatePeaks


CHANGES IN VERSION 1.5.4
------------------------

NEW FEATURES

    o plotTV can now plot expression profiles including introns triggered by the new option pre_mRNA

BUG FIXES

    o Fixed a bug which occurred if only two colors were passed to plotTV via colr


CHANGES IN VERSION 1.5.3
------------------------

NEW FEATURES

    o meltPeak can return loess smoothed scores.


CHANGES IN VERSION 1.5.2
------------------------

BUG FIXES

    o Fixed an issue with the gene names returned from gtf2gr.


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

BUG FIXES

    o The q-value cut off in macs2gr did not work as expected.


CHANGES IN VERSION 1.2.11
------------------------

BUG FIXES

    o Fixed a compilation problem related to the new Rsamtools version on windows.


CHANGES IN VERSION 1.2.9
------------------------

BUG FIXES

    o Updated vignette


CHANGES IN VERSION 1.2.8
------------------------

NEW FEATURES

    o meltPeaks() normalizes to Reads Per Million mapped reads after quality filtering according to the filtered_reads slot.
    o parseReads() now also returns the total and local base pairs covered which can be accessed by the slots gsize() and lsize() respectively.


CHANGES IN VERSION 1.2.7
------------------------

NEW FEATURES

    o New convenience function meltPeaks(), which returns a data frame with normalized peak densities suitable for plotting with ggplot2.

BUG FIXES

    o Minor help file corrections.


CHANGES IN VERSION 1.2.6
------------------------

BUG FIXES

    o macs2gr() supports relative distances instead of absolute distances reported by older MACS versions.


CHANGES IN VERSION 1.2.5
------------------------

BUG FIXES

    o annotatePeaks() did not accurately resolve ambiguities in some instances.


CHANGES IN VERSION 1.2.4
------------------------

BUG FIXES

    o gtf2gr() can now handle gene and transcript IDs with white spaces.


CHANGES IN VERSION 1.2.3
------------------------

NEW FEATURES

    o All slice methods can now return binned densities of predefined width.
    o The method to bin data can be specified by a new option in plotTV and the slice methods called bin_method. The amount of bins to be returned can be specified by nbins.
    o Default method to plot densities in plotTV is now mean instead of linear interpolation using approx. median or max are additional possibilities.


CHANGES IN VERSION 1.2.2
------------------------

BUG FIXES

    o Minor bug fix in plotTV


CHANGES IN VERSION 1.2.1
------------------------

BUG FIXES

    o Minor bug fix in plotTVData


CHANGES IN VERSION 1.2.0
------------------------


NEW FEATURES

    o A new class TVResults is returned by plotTV containing all important results of the clustering and plotting.
    o TVResults objects can be accessed by their slots and plotTVData. plotTVData returns a data frame with the summarized results.
    o Added option showPlot to plotTV() to suppress plotting optionally. This is useful if only the clustering results are needed.
    o Added an option name_width to plotTV() to enable customized widths of the row labels.

BUG FIXES

    o Improved kmeans clustering


CHANGES IN VERSION 1.1.6
------------------------

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 1.1.5
------------------------

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 1.1.4
------------------------

NEW FEATURES

    o All slice methods return NA instead of NULL in case of chromosome miss matches or negative query lengths.

BUG FIXES

    o Using toRle in the slice methods will work with missing values.


CHANGES IN VERSION 1.1.3
------------------------

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.

BUG FIXES

    o Improved type checking.


CHANGES IN VERSION 1.1.2
------------------------

NEW FEATURES

    o Added an option to gtf2gr which defines the GTF feature type entry to be filtered during parsing
    o gtf2gr also incorporates the gene_id if present in the input gtf file


CHANGES IN VERSION 1.1.1
------------------------

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 1.1.0
------------------------

BUG FIXES

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

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
