2.2.0

• plotFingerprint now iterates through line styles as well as colors. This allows up to 35 samples per plot without repeating (not that that many would ever be recommended). This was issue #80.
• Fixed a number of Galaxy wrappers, which were rendered incorrectly due to including a section title of "Background".
• A number of image file handles were previously not explicitly closed, which caused occasional completion of a plot* program but without the files actually being there. This only happened on some NFS mount points.
• The Galaxy wrappers now support the --outFileNameData option on plotProfile and plotHeatmap.
• Added support for blacklist regions. These can be supplied as a BED file and the regions will largely be skipped in processing (they'll also be ignored during normalization). This is very useful to skip regions known to attract excess signal. This was issue #101.
• Modified plotPCA to include the actual eigenvalues rather than rescaled ones. Also, plotPCA can now output the underlying values (issue #231).
• Regions within each feature body can now be unscaled when using computeMatrix. Thus, if you're interested in unscaled signal around the TSS/TES then you can now use the --unscaled5prime and --unscaled3prime options. This was issue #108.
• bamCoverage now has a --filterRNAstrand option, that will produce coverage for only a single strand. Note that the strand referred to is the DNA strand and not sense/anti-sense.
• Issues with plotHeatmap x-axis labels were fixed (issue #301).