Changes in version 2.0.6 (2015-06-15) o Fixed another bug resulting from checking whether all co-analyzed bams were mapped to the same reference genome ------------------------------------- Changes in version 2.0.5 (2015-06-10) o Fixed an error resulting from checking whether all co-analyzed bams were mapped to the same reference genome ------------------------------------- Changes in version 2.0.4 (2015-06-05) o Fixed an error in plotCNA leading to mixing of chromosomes during plotting ------------------------------------- Changes in version 2.0.3 (2015-05-06) o Included MAD-values in CopywriteR log file ------------------------------------- Changes in version 2.0.2 (2015-04-24) o Fixed the bug that under certain circumstances error messages are thrown that .bam files are not coordinate sorted ------------------------------------- Changes in version 2.0.1 (2015-04-18) o Implemented resetting the original work directory upon exit of CopywriteR functions o Corrected R dependency to version 3.2 o Updated DESCRIPTION file o Fixed bug resulting in failure to calculate loesses ------------------------------------- RELEASE (version 2.0) ------------------------------------- Changes in version 1.99.4 (2015-04-08) o Fixed bug related to logging when .bam are not indexed ------------------------------------- Changes in version 1.99.3 (2015-04-06) o Fixed bug related to testing of sort mode of .bam files ------------------------------------- Changes in version 1.99.2 (2015-03-21) o Provided vignette that allows R CMD CHECK --no-build-vignettes in <5 min o Fixed minor bug affecting runs in which not all samples are analyzed by CopywriteR function o Included a test for sorting of .bam files o Improved error messages o Fixed minor bug affecting plotting of samples o Fixed minor bug causing error when processing >100 samples simultaneously o Added support for capture regions bed files lacking the correct chromosome name prefix o Fixed minor bug affecting read count statistics on single-sample analysis ------------------------------------- Changes in version 1.99.0 (2015-03-05) o Released new version o Improved the speed of the package o Implemented logging with the futile.logger package o Replaced direct slot or field access with the use of accessor functions o Implemented text wrapping o Replaced the use of bed-file format with GRanges objects o Created annotation and experiment packages o Addressed all NOTES upon R CMD CHECK o Restore options upon exit o Adjusted version numbering to 1.99.0 o Implemented BiocParallel for parallel computing o Changed name from ENCODER to CopywriteR o Shortened lines to 80 characters o Added NEWS file o Changed F to FALSE o Changed T to TRUE o Added biocViews o Changed version to 0.99.0