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

NEW FEATURES

    o Added DNAcopy algorithm to Strand-seq mode.

SIGNIFICANT USER-LEVEL CHANGES

    o Renamed parameter 'most.frequent.state.bivariate' -> 'most.frequent.state.strandseq'.

    o Renamed parameter 'most.frequent.state.univariate' -> 'most.frequent.state'.

    o New parameter 'strandseq'.

BUG FIXES

    o Dendrogram and heatmap are now aligned properly in heatmapGenomewide().


CHANGES IN VERSION 1.1.5
------------------------

NEW FEATURES

    o Aneufinder runs DNAcopy algorithm in addition to the Hidden Markov Model.

    o New function "getQC" to get a data.frame with quality metrics.

SIGNIFICANT USER-LEVEL CHANGES

    o Changed folder structure to include DNAcopy method.

    o Renamed methods from c('univariate','bivariate') to c('HMM','biHMM')


CHANGES IN VERSION 1.1.4
------------------------

NEW FEATURES

    o karyotypeMeasures() has new option regions.

    o plotHeterogeneity() for easy plotting of karyotype measures.

    o BiocStyle vignette.

    o New option use.bamsignals=FALSE/TRUE available for the binning step.

    o getQC() handles NULL entries as NA and is thus more robust.

    o complexity estimation via Michaelis-Menten is carried along.

SIGNIFICANT USER-LEVEL CHANGES

    o Color scheme for copy number states has been improved for states >= 5-somy.

    o Option format has been removed in all functions. File format is determined
      automatically now.

    o clusterByQuality() clusters now on complexity as well by default.

DEPRECATED AND DEFUNCT

BUG FIXES

    o Corrected bug in order of seqlevels after as(..., 'GRanges').

    o Corrected bug in hotspotter() that caused detection of low-abundance hotspots.
