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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)