***** version 1.99.1 - 23 January 2013
· Package updated to be used in Bioconductor 3.1

***** version 1.7.2 - 23 January 2013
. Changed filterFFT-methods.R. Now filtering of regions is performed in iterative loop rather than with a recursive call. This improves dramatically the memory usage of long non-splitted regions.

***** version 1.5.0 - 01 October 2012
. changed from multicore to parallel package

***** version 1.2.2 - 23 March 2012
. 'mergeCalls' now uses the parameter 'min.overlap' instead of 'dyad.dist' for being coherent with the countOverlap calls from IRanges
. 'peakDetection' crashed when no values below threshold were available

***** version 1.2.1 - 01 March 2012
. Fixed memory usage and speed of function 'mergeCalls' 
. Added scale factor and other parameters to 'coverage.rpm'

***** version 1.2.0 - 15 November 2011
+ Added 'mergeCalls': automatic merging of close nucleosome calls
. Individual height and width score are returned in peakScoring, additionally to the mixed score
. PlotPeaks has now support for fuzzy nucleosomes and decomposite score
. Fixed malfunction of processReads in single-ended reads when using trim==fragmentLen

***** version 0.99.7 - 27 October 2011 (v.1.0RC2 for BioC 2.9)
. Improved performance (CPU and memory need) of fragmentLenDetect for large (human-ENCODE) datasets.

***** version 0.99.6 - 24 October 2011 (v.1.0RC for BioC 2.9) 
. Changed the score system in peakScoring for ranged data. Now different weigths for width and height score can be specified and the weighted sum of the scores is returned, instead the direct product of them.

***** version 0.99.5 - 13 October 2011
. Bug fix in the fragmentLenDetect which was returning wrong values, processReads could also be affected by this bug
+ processReads: Added custom parameters pass for fragmentLenDetect if fragmentLen=NULL
+ fragmentLenDetect: Added parameter as.shift to allow shift value return instead of the fragment length (the one by default)

***** version 0.99.4 - 01 August 2011
+ "threshold" in peak calling now can be set using percentage or a direct coverage value
. export.wig now only uses maximum 4 decimals to avoid creating big size wig files
. bugfixes in export.wig and export.bed
. increased default threshold for pcKeepCompDetect (old value was too restrictive)

***** version 0.99.3 - 19 July 2011
. bug fixes

***** version 0.99.2 - 17 July 2011
+ First version available in Bioconductor
+ CITATION file added
. filterFFT now returns a NA or 0 value in the same regions as the input has it
. pcKeepCompDetect now returns a value in the range pc.min:pc.max

***** version 0.99.1 - 11 July 2011
+ Added pcKeepCompDetect (automatic calculation of fitted component selection for filterFFT)
+ Added controlCorrection (correction of coverage profiles to avoid methodology biases)
. Correction of "multicore" library detection
. Correction of a bug in the filterFFT in joining large sequences
. filterFFT now takes as default pcKeepComp="auto"
. pcKeepCompDetect and controlCorrection added to vignette

***** version 0.99.0 - 28 june 2011
. Minor changes to satisfy Bioconductor requirements

***** version 0.2.1 - 27 april 2011
+ Added example code to all functions
. Fixes in export.wig function

***** version 0.2.0 - 18 april 2011
+ Added fragmentLenDetect (automatic calculation of sequenced fragments for single ended data)
+ Added syntheticNucMap (generation of random coverage maps)
. Minor corrections in other functions

**** version 0.1.3 - 02 february 2011
+ First public version
