2.5.0

• 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.