Deeptools

* `plotCoverage` now has a `--BED` option, to restrict plots and output to apply to a specific set of regions given by a BED or GTF file or files (issue 829).
* `plotCoverage` now has a `--DepthSummary` option, which produces a summary similar to GATK's DepthOfCoverage (issue 828).
* `plotCoverage` is now able to compute coverage metrics for arbitrary coverage thresholds using multiples of the `-ct` option (e.g., `-ct 0 -ct 10 -ct 20 -ct 30`).

* Changed a bug in `estimateReadFiltering` where the estimated number of filtered reads was typically too low.
* Made an internal change that should drastically reduce the memory requirements of many tools. This slightly increases run time, but as the resulting resource usage is much more attractive this is judged worthwhile.
* An informative error message is now produced with `bamCoverage` if RPGC normalization is requested but no effective genome size is provided (issue 815).
* Fixes some issues with y-axis scaling (issue 822)

* Added access in the Galaxy wrapper to the `--labels` option in most tools (issue 738)
* Added the `std` plot type to plotProfile in Galaxy (issue 782)
* `bamCompare` now has a `--skipZeroOverZero` option to allow skipping bins where both input files lack coverage (issue 785)
* `bamCompare` and `bigwigCompare` can now take two pseudocounts, in case you want a different value for the numerator and the denominator (issue 784)
* `multiBamSummary` now has a `--scaleFactors` option, which computes scale factors in the same manner as DESeq2 to a file. Note that the produced scaling factors are meant to be used with `bamCoverage`. If you want to use them directly in DESeq2 (or a similar package) you will need to invert them (take 1/scale factor). (issue 800)
* Fixed an issue with large numbers of samples and small genome sizes sometimes causing nothing to be processed. (issue 801)

* Added the `--legendLocation` option in the Galaxy wrappers for plotProfile and plotHeatmap
* More thoroughly checked that output files can be written (issue 764).
* `bamCompare` and `bigwigCompare` can now take two pseudocounts, in case you want a different value for the numerator and the denominator (issue 784)

* Added a `--markers` option to `plotPCA`, courtesy of sklasfeld.
* `computeMatrixOperations rbind` now properly supports multiple region groups (issue 742)
* Fixed the usage of `--xRange` and `--yRange` with `plotCorrelation` (issue 709)

* Fixed the `--outFileNameData` option in `plotProfile` when `computeMatrix reference-point --referencePoint center` was used. This caused an error previously. (issue 727)
* RPGC normalization and the `--scaleFactor` option in `bamCoverage` are no longer mutually exclusive.
* Increased the default plot width in plotPCA (issue 738)