Three changes:

1. Added a new parameter to the segmentation tools for microarrays and NGS data. (These tools are otherwise identical, but the default value for this new parameter is different.)

2. Tool common/R-2.15/acgh-count-overlapping-cnvs.R has been updated to use the updated version of Database of Genomic Variants. The new tool downloads files directly from their web site, but previously these have been stored in tools/DGV. If local files are preferred, the URLs listed in the code should be downloaded, lines using remote URLs commended out, lines reading local files updated for new file names and uncommented.

3. Small change to output format of tool microarray/R-2.12/add-locations-to-data.R: name of output column "chr" changed to "chromosome" to be more consistent with other tools.

4. This one is not a new modification, but directory tools/FREEC_Linux64 is not used anymore. If it's still included in the distribution, it could be deleted shaving off 8.9 GB from the tools image.