Changes in version 1.12.0
-------------------------

RELEASE

    o Bioconductor 3.5

IMPROVEMENTS

    o VCF and SEG file export have been implemented to allow use of 
      downstream analysis tools such as Cartegenia (NGS) Bench.

    o binReadCounts() now supports parallel computing

    o calculateBlackListByRegions() has been implemented for convient 
      bin overlap calculation of any set of regions.
      

Changes in version 1.10.0
-------------------------

RELEASE
   
    o Bioconductor 3.4


Changes in version 1.8.0 (2016-05-04)
-------------------------------------

RELEASE

    o Bioconductor 3.3

IMPROVEMENTS

    o estimateCorrection(), segmentBins(), createBins(), and
      calculateBlacklist() now support parallel computing
      (see vignette for more details)

    o callBins() can now also use cutoffs instead of CGHcall

    o binReadCounts() now contains parameter pairedEnds to specify when using
      paired-end data, so that expected variance can be calculated correctly

    o segmentBins() now allows seeds for random number generation to be
      specified for reproducibility

    o binReadCounts() supports chunked processing of bam files

    o estimateCorrection() now also allows correcting for only GC content or
      mappability

BUG FIXES 

    o applyFilters() and highlightFilters() now work properly when using a
      numerical value for parameter residual

    o highlightFilters() no longer highlights entire chromosomes for which
      the residual filter is missing altogether, which matches the behavior of
      applyFilters()

    o getBinAnnotations() now allows custom bin annotations to be loaded via
      the path parameter even when an annotation package has been installed

    o phenodata files with a single variable are now handled correctly

    o calculateMappability() now retains correct chromosome order even when
      bigWigAverageOverBed reorders them

    o calculateBlacklist() now correctly handles non-integer chromosome names

Changes in version 1.6.0 (2015-10-14)
-------------------------------------

RELEASE

    o Bioconductor 3.2

IMPROVEMENTS

    o chromosomes() no longer tries to return chromosome names as an integer
      vector, but returns a character vector instead

BUG FIXES

    o plot() and calculateMappability() now work also for other chromosome
      names besides numbers and "X", "Y", and "MT"

Changes in version 1.4.2 (2015-08-20)
-------------------------------------

BUG FIXES

    o createBins() now properly selects chromosomes when ignoring 
      mitochondrial DNA. Please note that the mitochondrial DNA is only 
      ignored when it is called either "chrMT", "chrM", "MT", or "M"

Changes in version 1.4.1 (2015-06-30)
-------------------------------------

IMPROVEMENTS

    o correctBins() now filters out bins with missing loess correction estimate

Changes in version 1.4.0 (2015-04-17)
-------------------------------------

RELEASE

    o Bioconductor 3.1

Changes in version 1.2.4 (2015-01-21)
-------------------------------------

OTHER

    o update package maintainer

Changes in version 1.2.3 (2015-01-20)
-------------------------------------

BUG FIXES

    o createBins() now also works for species not supported by GenomeInfoDb
      (such as Canis lupus familiaris)

Changes in version 1.2.2 (2014-12-23)
-------------------------------------

IMPROVEMENTS

    o applyFilters() now ignores the residual filter for chromosomes for which
      it does not exist (instead of always filtering out the entire chromosome)

Changes in version 1.2.1 (2014-11-01)
-------------------------------------

IMPROVEMENTS

    o add an asterisk in the noise measure to clarify it's not a regular
      standard deviation or variance, but first scaled with the mean (so that
      the mean is 1.0 and the relationship holds between variance and 1/N, where
      N is the average number of reads per bins)

    o clarify the use of log2/sqrt transformation in segmentBins()

Changes in version 1.2.0 (2014-10-14)
-------------------------------------

RELEASE

    o Bioconductor 3.0

IMPROVEMENTS

    o segmentBins() supports another transformation option besides log2:
      sqrt(x + 3/8), which stabilizes the variance

    o plot() can skip plotting of segments and calls by specifying
      doSegments=FALSE and doCalls=FALSE

    o exportBins() also supports BED files

BUG FIXES

    o exportBins() saves base pair positions in fixed notation instead of
      scientific

Changes in version 1.0.5 (2014-06-13)
-------------------------------------

BUG FIXES

    o fix a bug caused by package matrixStats changing madDiff() from an S4
      to an S3 method in version 0.9.4, released on 2014-05-23

Changes in version 1.0.4 (2014-05-23)
-------------------------------------

BUG FIXES

    o getBinAnnotations() fixed after being broken by a change in Bitbucket

Changes in version 1.0.3 (2014-05-23)
-------------------------------------

IMPROVEMENTS

    o added exportBins() for exporting to a file

    o switch graphics in the vignette to PNG

Changes in version 1.0.2 (2014-05-15)
-------------------------------------

IMPROVEMENTS

    o plot() honors user-specified values for xlab and xaxt

    o plot() allows omission of labels for the standard deviation and
      the number of data points

    o improve diagnostic messages

Changes in version 1.0.1 (2014-04-17)
-------------------------------------

BUG FIXES

    o smoothOutlierBins() correctly ignores bins filtered out

Changes in version 1.0.0 (2014-04-14)
-------------------------------------

RELEASE

    o initial release as part of Bioconductor 2.14
