2.2.1

 * 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.

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).

2.1.1

 * 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.

2.1.0

 * 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.
 
2.0.1

 * A critical bug that prevented plotPCA from running was fixed.
 * multiBamCoverage was renamed to multiBamSummary, to be in better alignment with multiBigwigSummary.
 * computeGCBias and correctGCBias are now more tolerant of chromosome name mismatches.
 * multiBigwigSummary and multiBamSummary can accept a single bigWig/BAM input file, though one should use the
   --outRawCounts argument.

2.0.0

 * Documentation improved and migrated to http://deeptools.readthedocs.org The API to use deepTools modules is now
   part of the documentation and includes a tutorial.
 * Allow multiple bigwig files in computeMatrix that can be clustered together
 * computeMatrix now accepts multiple bed files. Each bed file is considered as a group. Labels are automatically
   added based on the file names.
 * When computing read coverage now splited reads are understood. This is convenient for computing the
   coverage of for RNA-seq data.
 * New quality control tool 'plotCoverage' to plot the coverage over base pairs for multiple samples
 * renaming of --missingDataAsZero to --skipNonCovered regions for clarity in bamCoverage and bamCompare
 * New analysis tool plotPCA that visualizes the results from principal component analysis
 * New option in bamCoverage `--MNase` that will compute the read coverage only considering 2 base pairs at the
   center of the fragment.
 * Make read extension optional. Remove the need to specify a default fragment length for most of the tools. Now, when
   read extension is enabled and the bam files contain paired en data, the mean fragment length is automatically
   calculated by sampling the read pairs in the bam file. The --doNotExtendPairedEnds and --fragmentLentgh parameters
   are no longer used and the new --extendReads parameter was added.
 * Dramatically improved bigwig related tools by using the new pyBigWig module. Eliminated the requirement for the
   UCSC program `bigWigInfo`
 * renamed heatmapper to plotHeatmap and profiler to plotProfile
 * added hierarchical clustering, besides k-means to plotProfile and plotHeatmap
 * improved plotting features for plotProfile when using 'overlapped_lines' and 'heatmap' plot types
 * Resolved an error introduced by numpy version 1.10 in computeMatrix
 * plotting of correlations (from bamCorrelate or bigwigCorrelate) was separated from the computation of the
   underlying data. A new tool, plotCorrelation was added. This tool can plot correlations as heatmaps or as scatter
   plots and includes options to adjust a large array of visual features.
 * Fixed issue with bed intervals in bigwigCorrelate and bamCorrelate and a user specified region.
 * Correlation coefficients can be computed even if the data contains NaNs
 * Allow computeMatrix to read files with DOS newline characters
 * Added option --skipChromosomes to  bigwigCorrelate, for example to skip all 'random' chromosomes. bigwigCorrelate
   now also considers chromosomes as identical when their names between samples differ with the prefix 'chr'. E.g.
   chr1 vs. 1
 * For bamCoverage and bamCompare, behaviour of scaleFactor was updated such that now, if given in combination
   with the normalization options (normalize to 1x or normalize using RPKM) the given scaleFactor
   will multiply the scale factor computed for the normalization methods.
 * Fixed problem with read pairs labelled as proper pairs by the aligner but that were actually not proper pairs, for
   example because the mates did not face each other. deepTools adds further checks to determine if a read pair is a
   proper pair.
 * Added titles to QC plots (#74)
 * Added --samFlagInclude and --samFlagExclude parameters. This is useful to for example only include forward reads
 * In deeptools2 most of the core code was rewriting to facilitate API usage and for optimization.
