Added some plotting options for CN survival plots.
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
More memory efficient copy number calling and preliminary support for homozygous deletions.
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Plots now use sample names from phenodata and PNG instead of PDF (which were sometimes huge).
One small cosmetic change.
The generated PDF now contains raster images instead of vector. Requires installation of the 'png' library for R-2.15_bioc-2.11.
Merge remote-tracking branch 'upstream/master'
Merge pull request #12 from ilarischeinin/master

Miscellaneous copy number updates