3.1.0

• The --centerReads option in bamCoverage is now compatible with --Offset (previously --centerReads was silently ignored if --Offset was specified). (issue #693)
• bamCoverage and bamCompare now have an --exactScaling option. Instead of using a random sample of alignment to compute the scaling factor, this causes all reads in the file to be used. This is significantly slower, but helpful in situations where reads that should be excluded clump together on the genome (i.e., when sampling based on location is likely to be inaccurate).
• plotCorrelation --whatToPlot scatterplot now has --xRange and --yRange options rather than just --maxRange. (issue #709)
• computeMatrixOperations can now be used to change sample and group names.
• computeMatrixOperations can now filter rows by minimum and/or maximum value.
• --maxThreshold and --minThreshold are now more consistently honoured. (#702)
• Fixed region handling when using files on deepBlue (#700)
• Using --normalizeUsing RPGC with bamCompare will now result in a fatal error, rather than a simple warning and the settings being changed under the hood. (#718)
• Related to the last point, setting --normalizeUsing to anything other than None will result in an error unless --scaleFactorsMethod None is also used. This is to prevent people from accidentally getting unintended normalization.
• bamPEFragmentSize no longer exploids its memory use with multiple large BAM/CRAM files (#720). Many other tools will also benefit from this change.