Fixed bug

This release fixes a bug that is encountered when using more sample / control combinations than the number of unique samples + controls. The specific error message that is given when encountering this error is the following:

Error in [<-.data.frame(*tmp*, , "off.target", value = c(XXX, XXX, :
replacement has X rows, data has X

Please use version 2.6.1 for compatibility with earlier versions of Bioconductor and 2.9.0 for compatibility with later ones, including the current version.

Reuse intermediate files

This is a pre-release version that should allow one to reuse filtered bams (which can be obtained by setting the keep.intermediary.files argument to TRUE) when samples are to be analyzed multiple times (for instance to optimize the bin size for samples).

Improved testing for mapping to same reference genome for all bams

This version removes another error related to the testing whether all bams have been aligned to the same reference genome, and can prevent getting the error message that

"The bam files have been mapped to different reference genomes (the chromosome names are not identical). Please run only .bam files mapped to the same reference genome together."

Improved testing for mapping to same reference genome for all bams

Fixed a bug stemming from checking whether all bam files have been mapped to the same reference genome

Fixed a bug resulting in mixing of chromosomes during plotting

This release fixes the problem that, depending on the version of an installed dependency, chromosomes are mixed during plotting of the data using plotCNA.

Included MAD-values in CopywriteR log file

Included MAD-values in CopywriteR log file

Reinstalled bug fix in testing sort mode of .bam files

This release fixes the bug that under certain circumstances error messages are thrown that .bam files are not coordinate sorted.

Fixed a bug related to bin-spanning peaks

In Bioconductor release (version 2.0.0) amended the following:

• reset the original work directory on exit of CopywriteR functions
• fixed a bug that originates from the introduction of NAs in the read.counts variable by wide peaks spanning full bins. This results in the error message:

Error in value[[3L]](cond): The GC-content and mappability normalization did not work due to a failure to calculate loesses. This can generally be solved by using larger bin sizes. Stopping execution of the remaining part of the script...

Fixed a bug related to analysis of non-indexed .bam files

This version fixes a bug that occurs upon analysis of non-indexed .bam files. In addition, it improves the output of the log-file.

Fixed a bug in testing sort mode of .bam files

This release fixes the bug that under certain circumstances error messages are thrown that .bam files are not coordinate sorted.