Deeptools

* Updated blacklist handling such that an error is thrown on overlapping regions.

* Fixed issue 612, which only occurs when unaligned reads have a position assigned to them.
* Ticks in the profile plot at the top of the output of `plotHeatmap` should now always line up properly. (issue 616)

* Fixed a bug in `plotEnrichment`, the `--keepExons` option with a BED12 file would cause an error. (issue 559)
* `bamCoverage` now doesn't cause and error to be thrown by `sort` in there are "/spaces in quoted path/". (issue 558)

* Fixed a bug in `bamCoverage` that can cause crashes when python3 is used.
* Fixed a bug in the multiBigwigSummary Galaxy wrapper.
* A more reasonable exit code (not 0) is now returned if there's a mismatch in the label and file number.
* `plotFingerprint` no longer tries to use illegal line designators (issue 538)
* Various documentation fixes

* Added universal new line support to deeptoolsintervals (issue 506).
* Fixed a few issues with correctGCBias under python 3.5 (thanks to drakeeee)
* Setting `--minThreshold 0.0` or `--maxThreshold 0.0` now works properly. Previously, setting either of these to 0 was ignored. (issue 516)
* You can now specify the plot width and height in `plotPCA` and `plotCorrelation` (heatmap only) with the `--plotWidth` and `--plotHeight` parameters. (issue 507)
* plotCoverage no longer clips the top off of plots. Further, you can now set the plot width and height with `--plotWidth` and `--plotHeight`. (issue 508)
* In bamCoverage, specifying `--filterRNAstrand` no longer results in `--extendReads` being ignored. (issue 520)
* `plotFingerprint` and `plotEnrichment` no longer require producing a plot, which is useful if you only need QC metrics and are using a LOT of samples (such that matplotlib would crash anyway). This hasn't been implemented in Galaxy, but can if people would like it. (issues 519 and 526)
* `computeMatrix` now accepts a `--samplesLabel` option, which is useful in those cases when you aren't immediately running `plotHeatmap` and don't have terribly descriptive file names (issue 523)
* If you use `plotFingerprint` with the `--JSDsample` option and forget to list that file under `--bamfiles` it will be added automatically and the file name added to the labels if needed (issue 527)
* Various Galaxy wrapper fixes

* Fix a bug where using regions with the same name in multiple BED files in computeMatrix caused downstream problems in plotHeatmap/plotProfile (issue 477).
* If computeMatrix/plotHeatmap/plotProfile is asked to sort the output matrix, it now does so by ignoring NaN values. Previously, any row with an NaN was placed at the top of the output (issue 447).
* Fixed issue 471
* Various Galaxy wrapper fixes
* There is now a `--rowCenter` option in `plotPCA`, which can be used to make each row of the matrix used in the PCA to have a mean of 0. This can be useful in cases where there's extreme region-based depth variation that is shared between all samples. This was issue 477.
* The --Offset option is now available in `plotEnrichment`. This was issue 481.
* The maximum coverage allowed while calculating the Jensen-Shannon distance in `plotFingerprint` has been increased to 2 million and an informational message containing the number of bins above this value is printed to the standard output.
* `bamCoverage` now respects the `--scaleFactor` argument even if not other normalization is performed (issue 482).
* The `--minFragmentLength` and `--maxFragmentLength` options now respect single-end reads. For SE reads, these parameters refer to the number of aligned bases (i.e., splicing is ignored). This was issue 489.
* `--yMin` and `--yMax` can now be lists of values in `plotHeatmap`. This was issue 487. Note that the plots are not perfectly aligned if you do this.