* plotCorrelation` now has `--log1p` and `--maxRange` options if a scatter plot is produced. `--log1p` plots the natural log of the values (plus 1). `--maxRange` sets the maximum X and Y axis ranges. If they would normally be below this value then they are left unchanged. (issue 536)
* The PCA plot now includes "% of var. explained" in the top axis labels. (issue 547)
* `plotProfile` and `plotHeatmap` now have a `--labelRotation` option that can rotate the X-axis labels. This is one of the more common requests for customization. For further customization, please modify your .matplotlibrc file or save as a PDF and modify further in Illustrator or a similar program. (issue 537)
* The `--ignoreDuplicates` algorithm has been updated to better handle paired-end reads. (issue 524)
* Added the `estimateReadFiltering` tool to estimate how many reads would be filtered from a BAM file or files if a variety of desired filtering criterion are applied (issue 518).
* Rewrote the bigWig creation functions so there are no longer steps involving creating a single large bedGraph and then sorting it. That was a hold-over from previous versions that used UCSC tools. This was issue 546. This also means that there are no longer any required external programs (previously, only `sort` was required).
* `plotPCA` can now be run on the transposed matrix, as is typically done with RNAseq data (e.g., with deepTools). Further, matplotlib is now no longer used for computing the PCA, but rather an SVD is performed and the results directly used. The options `--transpose` and `--ntop` were also added. The former computes the PCA of the transposed matrix and the latter specifies how many of the most variable rows in the matrix to use. By default, the 1000 most variable features are used. In the (now optional) plot, the `--PCs` option can now be used to specify which principal components to plot. Finally, the unbiased standard deviation is used in the out, as is done by `prcomp()` in R. This was issue 496.
* Symbol colors for `plotPCA` can now be specified. (issue 560)
* `plotFingerprint` always returns the synthetic JSD, even if no `--JSDsample` is specified. (issue 564)
* `plotEnrichment` will only read in annotation files a single time rather than in each thread. This prevents terrible performance when using many tens of millions of BED/GTF regions at the expense of a slight memory increase. (issue 530)
* Fixed a small bug generally affecting `plotFingerprint` where BAM files without an index were processed as bigWig files, resulting in a confusing error message (issue 574). Thanks to Sitanshu Gakkhar for poiting this out!
* `bamPEFragmentSize` now has `--table` and `--outRawFragmentLengths` options. The former option will output the read/fragment metrics to a file in tabular format (in addition to the previous information written to the screen). The latter option will write the raw read/fragment counts to a tsv file. The format of the file is a line with "bamPEFragmentSize", followed by a header line of "Size\tOccurences\tSample", which should facilitate processing in things like R. (issue 572)
* `bamPEFragmentSize` will now plot the read length distribution for single-end BAM files. Note that if you mix single and paired-end files that the resulting plots may be difficult to interpret.
* The various plot commands do not actually have to plot anything, instead they can optionally only print their raw metrics or other text output. This is mostly useful with large numbers of input files, since the resulting plots can become quickly crowded. (issue 5719
* Expanded the metrics output by `bamPEFragmentSize` such that it now fully replaces Picard CollectInsertSizeMetrics (issue 577).
* "plotly" is now available as an output image format for all tools. Note that this is not really an image format, but rather an interactive webpage that you can open in your browser. The resulting webpages can be VERY large (especially for `plotHeatmap`), so please keep that in mind. Further, plotly does not currently have the capabilities to support all of deepTools' features, so note that some options will be ignored. For privacy reasons, all plotly files are saved locally and not uploaded to the public plot.ly site. You can click on the "Export to plot.ly" link on the bottom right of plotly output if you would like to modify the resulting files.
* `bamCoverage` no longer prints `normalization: depth` be default, but rather a more accurate message indicating that the scaling is performed according to the percentage of alignments kept after filtering. This was originally added in 366 (issue 590).
* The output of `plotFingerprint --outRawCounts` now has a header line to facilitate identification by MultiQC.
* `plotPCA` now has a `--log2` option, which log2 transforms the data before computing the PCA. Note that 0.01 is added to all values to 0 doesn't become -infinity.
* `computeGCBias` no longer requires a fragment length for paired-end datasets. This was apparently always meant to be the case anyway. (issue 595)
* `computeMatrixOperations sort` can now properly perform filtering of individual regions, as was originally intended (issue 594)
* `plotCoverage --outRawCounts` now has another line it its header, which is meant to aid MultiQC.
* There is no longer a configuration file. The default number of threads for all tools is 1. See issue 613.
* `bamCoverage` and `bamCompare` have rewritten normalization functions. They have both added CPM and BPM normalization and, importantly, filtering is now done **before** computing scaling factors. A few of the options associated with this (e.g., `--normalizeUsingRPKM`) have been replaced with the `--normalizeUsing` option. This behavior represents a break from that seen in earlier versions but should be easier to follow and more in line with what users expect is happening. The syntax for normalization has been reworked multiple times (see 629).
* Fixed issue 631
* `computeMatrix` now repeats labels for each column in a plot. This is convenient if you later want to merge reference-point and scale-regions runs and still have correct tick marks and labels in plotHeatmap/plotProfile (issue 614). Note that the output of computeMatrix and computeMatrixOperations can not be used with older versions of deepTools (but output from previous versions can still be used).
* `plotHeatmap --sortRegions` now has a `keep` option. This is identical to `--sortRegions no`, but may be clearer (issue 621)
* `plotPCA --outFileNameData` and `plotCorrelation --outFileCorMatrix` now produce files with a single comment line (i.e., 'plotPCA --outFileNameData' and 'plotCorrelation --outFileCorMatrix'). These can then be more easily parsed by programs like MultiQC.
* All functions that accept file labels (e.g., via a `--samplesLabel` option) now also have a `--smartLabels` option. This will result in labels comprised of the file name, after stripping any path and the file extension. (issue 627)
* The `-o` option can now be universally used to indicate the file to save a tool's primary output. Previously, some tools use `-o`, some used `-out` and still others used things like `-hist` or `-freq`. This caused annoyance due to having to always remember the appropriate switch. Hopefully standardizing to `-o` will alleviate this. (issue 640)
* Using a --blackListFileName with overlapping regions will typically now cause the various deepTools programs to stop. This is to ensure that resulting scale factors are correct (issue 649)
* `bamCoverage` is a bit more efficient with small BAM files now due to underlying algorithmic changes. Relatedely, bamCoverage will skip some unnecessary estimation steps if you are not filtering reads, further speeding processing a bit. (issue 662)
* Added support for CRAM files. This requires pysam > 0.13.0 (issue 619).