Package: QDNAseq
----------------

Version: 1.33.1 [2022-04-27]

MISCELLANEOUS:

 * Now the package gives an informative error message when an outdated
   version of the 'future' package is used.  It requires future (>=
   1.22.1).

BUG FIXES:

 * A few functions used class(x) == "data.frame" rather than
   inherits(x, "data.frame").
 

Version: 1.33.0 [2022-04-26]

 * The version number was bumped for the Bioconductor devel version,
   which is now BioC 3.16 for R-devel.


Version: 1.32.0 [2022-04-26]

 * The version number was bumped for the Bioconductor release version,
   which is now BioC 3.15 for R (>= 4.2.0).


Version: 1.31.0 [2021-10-27]

RELEASE:

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.15 for R-devel.


Version: 1.30.0 [2021-10-27]

RELEASE:

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.14 for R (>= 4.1.1).


Version: 1.29.6 [2021-10-23]

BUG FIXES:

 * segmentBins() would *report* the sample names as "NA" in output messages
   if the sample name contained hyphens, or other symbols automatically
   replaced by data.frame(..., check.names = TRUE).  This was a harmless bug.


Version: 1.29.5 [2021-10-20]

PERFORMANCE:

 * All internal row and column-based matrixStats calls now avoid overhead
   from handling row and column names.
 
MISCELLANEOUS:

 * Moved 'future' from Imports to Suggests.
 

Version: 1.29.4 [2021-10-16]

DOCUMENTATION:

 * Vignette now illustrate parallelization using the 'multisession' future
   strategy, instead of the deprecated 'multiprocess' strategy.

DEPRECATION AND DEFUNCT:

 * Argument 'seeds' of segmentBins() is defunct.  It has been deprecated and
   ignored since QDNAseq 1.21.3 (September 2019).


Version: 1.29.3 [2021-10-04]

NEW FEATURES:

 * Now argument 'logTransform' of exportBins() is ignored if 'type' = "calls".

 * Now exportBins() returns the pathname to the files written.

SOFTWARE QUALITY:

 * Test code coverage was increased from 42% to 52%.
 
 * Add package test for exportBins().

BUG FIXES:

 * exportBins(fit, format = "seg", ...) and format = "vcf" would merge
   segments with equal copy-number calls if they were interweaved with
   copy-neutral segments.

 * exportBins(fit, format = "seg", ...) and format = "vcf" produced an obscure
   error with messages "Error in dimnames(x) <- dn : length of 'dimnames' [2]
   not equal to array extent" for samples with no copy-number abberations.
   
 * exportBins(fit, format = "seg", file = ...) and format = "vcf" did not
   respect argument 'file' but instead wrote files of its own names to the
   current working directory.
   
 * exportBins() would corrupt option 'scipen'.  Now it is left unchanged.

KNOWN ISSUES:

 * callBins() produces warnings on "Recycling array of length 1 in vector-
   array arithmetic is deprecated. Use c() or as.vector() instead." in
   R (>= 3.4.0).  This is a problem in the package 'CGHcall' dependency and
   is something that needs to be fixed there.  For further details, please
   see https://github.com/tgac-vumc/CGHcall/issues/2.


Version: 1.29.2 [2021-09-22]

SOFTWARE QUALITY:

 * Test code coverage was increased from 32% to 39%.

 * Added package tests for binReadCounts().

BUG FIXES:

 * binReadCounts() would fail when specifying argument 'chunkSize'.  The fix
   was to require 'future' package version 1.22.1 or newer.
 

Version: 1.29.1 [2021-08-26]

SOFTWARE QUALITY:

 * Add package test for binReadCounts().


Version: 1.28.0 [2021-05-19]

RELEASE:

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.13 for R (>= 4.0.3).


Version: 1.26.0 [2020-10-28]

RELEASE:

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.12 for R (>= 4.0.0).


Version: 1.24.0 [2019-10-30]

RELEASE:

 * The version number was bumped for the Bioconductor release version, which is
   now BioC 3.11 for R (>= 3.6.1).


Version: 1.22.0 [2018-10-30]

RELEASE:

 * Bioconductor 3.10


Version: 1.21.6 [2019-09-25]

BUG FIXES:

 * Link to the 'GEM library' tool was broken.
 

Version: 1.21.5 [2019-09-09]

BUG FIXES:

 * plot(..., logTransform=TRUE, doSegments=TRUE) on QDNAseqSignals would
   position segments that were out of range incorrectly, because it forgot
   to take the log transform on those outliers.
 

Version: 1.21.4 [2019-09-06]

SIGNIFICANT CHANGES:

 * Bin annotation data files are no longer downloaded automatically. They
   are instead part of Bioconductor annotation packages QDNAseq.hg19 and
   QDNAseq.mm10, which needs to be installed by the user.  If not installed,
   an error is now produced.  The reason for this change, is that the
   QDNAseq maintainers will no longer host QDNAseq bin annotation files
   online (in the cloud).


Version: 1.21.3 [2019-09-04]

NEW FEATURES:

 * All functions that produce verbose output gained argument 'verbose'.  For
   backward compatibility, it currently defaults to 'verbose=TRUE' but that
   may be changed to 'verbose=FALSE' in a future release.

IMPROVEMENTS:

 * callBins() now respects option 'QDNAseq::verbose' for controlling whether
   output from the CGHcall package should be relayed or not.
   
 * MEMORY: Utilize more memory-efficient matrixStats functions colSums2(),
   colMeans2(), etc.

DEPRECATION AND DEFUNCT:

 * Argument 'seeds' of segmentBins() is deprecated because it did not use
   proper parallel random number generation (RNG).  We now instead rely on
   future.apply::future_lapply(..., future.seed=TRUE) for this.


Version: 1.21.2 [2019-09-03]

SIGNIFICANT CHANGES:

 * Package now imports the 'future' and 'future.apply' packages; previously
   the 'future' was listed as a suggested package.

 * Package no longer depends on BiocParallel.

 * binReadCounts() now uses the future framework instead of BiocParallel for
   parallelization.

IMPROVEMENTS:

 * MEMORY: Avoiding data type coercions in more places by for instance making
   sure that vectors and matrices are initated with the values of the correct
   data type (instead of the default NA, which is a logical value).

SOFTWARE QUALITY:

 * Using future_lapply() and future_apply() of the well-tested future.apply
   package instead of internal analogue implementations.

 * TESTS: Now testing numerical reproducibility also for parallel processing
   (using future strategies 'multisession' and 'multicore').

 * TESTS: Now asserting numerical reproducibility of also segmentBins() and
   callBins().
 

Version: 1.21.1 [2019-08-30]

SIGNIFICANT CHANGES:

 * exportVCF() is no longer exported. Use exportBins(..., format="vcf")
   instead.
 

Version: 1.20.0 [2019-05-02]

RELEASE:

 * Bioconductor 3.9


Version: 1.18.0 [2018-10-30]

RELEASE:

 * Bioconductor 3.8


Version: 1.16.0 [2018-04-30]

RELEASE:

 * Bioconductor 3.7


Version: 1.14.0 [2017-10-30]

RELEASE:

 * Bioconductor 3.6


Version: 1.12.0 [2017-04-23]

RELEASE:

 * Bioconductor 3.5

IMPROVEMENTS:

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

 * binReadCounts() now supports parallel computing

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

Version: 1.10.0 [2016-10-18]

RELEASE:
   
 * Bioconductor 3.4


Version: 1.8.0 [2016-05-04]

RELEASE:

 * Bioconductor 3.3

IMPROVEMENTS:

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

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

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

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

 * binReadCounts() supports chunked processing of bam files

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

BUG FIXES:

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

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

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

 * phenodata files with a single variable are now handled correctly

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

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


Version: 1.6.0 [2015-10-14]

RELEASE:

 * Bioconductor 3.2

IMPROVEMENTS:

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

BUG FIXES:

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


Version: 1.4.2 [2015-08-20]

BUG FIXES:

 * 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"


Version: 1.4.1 [2015-06-30]

IMPROVEMENTS:

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

Version: 1.4.0 [2015-04-17]


RELEASE:

 * Bioconductor 3.1

Version: 1.2.4 [2015-01-21]

OTHER:

 * update package maintainer

Version: 1.2.3 [2015-01-20]

BUG FIXES:

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


Version: 1.2.2 [2014-12-23]

IMPROVEMENTS:

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


Version: 1.2.1 [2014-11-01]

IMPROVEMENTS:

 * 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)

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


Version: 1.2.0 [2014-10-14]

RELEASE:

 * Bioconductor 3.0

IMPROVEMENTS:

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

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

 * exportBins() also supports BED files

BUG FIXES:

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


Version: 1.0.5 [2014-06-13]

BUG FIXES:

 * 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


Version: 1.0.4 [2014-05-23]

BUG FIXES:

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


Version: 1.0.3 [2014-05-23]

IMPROVEMENTS:

 * added exportBins() for exporting to a file

 * switch graphics in the vignette to PNG


Version: 1.0.2 [2014-05-15]

IMPROVEMENTS:

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

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

 * improve diagnostic messages


Version: 1.0.1 [2014-04-17]

BUG FIXES:

 * smoothOutlierBins() correctly ignores bins filtered out


Version: 1.0.0 [2014-04-14]

RELEASE:

 * initial release as part of Bioconductor 2.14