Deeptools

* Fixed issue 334, where computeGCBias wasn't properly handling the black list option.

* Fixed labels when hierarchical clustering is used (they were off by one previously).
* Fixed a bug wherein bamCompare couldn't work with a blacklist
* Fixed yet another change in pysam, though at least in this case is was fixing a previous problem

* Fixed a bug introduced in version 2.2.0 wherein sometimes a pre-2.2.0 produced matrix file could no longer be used with plotHeatmap or plotProfile (this only happened when --outFileNameData was then used).
* Finally suppressed all of the runtime warnings that numpy likes to randomly throw.
* Worked around an undocumented change in pysam-0.9.0 that tended to break things.

* 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).

* Fixed a how the --hclust option was handled in plotHeatmap/plotProfile. This gets around a quirk in scipy.
* A bug involving processing comment lines in BED files was corrected (issue 288)
* The Galaxy wrappers are now automatically tested with each modification.
* plotCoverage and plotFingerprint in Galaxy now accept 1 or more BAM files rather than at least 2 files.

* Updates to many of the Galaxy wrappers and associated documentation.
* A bug was fixed in how chromosome names were dealt with in bigWig files. If you ever received errors due to illegal intervals then that should now be fixed. This was issue 250
* plotProfile now has an --outFileNameData option for saving the underlying data in a text format.
* correctGCBias ensures that the resulting BAM file will pass picard/HTSJDK's validation if the input file did (issue 248)
* The default bin size was changed to 10, which is typically a bit more useful
* The --regionsLabel option to plotProfile and plotHeatmap now accepts a space-separated list, in line with --samplesLabel
* BAM files that have had their sequences stripped no longer cause an error
* bamPEFragmentSize now has -bs and -n options to allow adjusting the number of alignments sampled. Note that the default value is auto-adjusted if the sampling is too sparse.
* bamPEFragmentSize now accepts single-end files.
* The --hclust option to plotProfile and plotHeatmap continues even if one of the groups is too small for plotting (matplotlib will produce a warning that you can ignore). This was issue 280.