2.4.0

• The --Offset option to bamCoverage can now take two values, which can be used to specify a range within each alignment of bases to use. As an example, --Offset 5 -1 will use ignore the first 4 bases of an alignment (accounting for orientation) and use only the 5th through last base. This can be useful for things like ATACseq (see #370).
• Read extension can now be used in conjunction with --Offset in bamCoverage.
• plotFingerprint can now output quality metrics, including the Jensen-Shannon distance if a reference sample is specified (see #328). Additionally, various statistics from CHANCE can be produced.
• Switched from using the 'twobitreader' python module to our new custom 'py2bit' module for accessing 2bit files. This fixes the performance regression seen in computeGCBias starting in version 2.3.0 (#383).
• bigwigCompare, computeMatrix, and multiBigwigSummary can read signal files hosted on deepBlue.
• Fixed a minor bug in deeptools, where the --version option was ignored (see #404).
• Text in SVG and PDF files is now actual text and not a path (see #403).
• The --maxFragmentLength option in bamCoverage now alters the maxPairedFragmentLength that is otherwise hard-coded (see #410).
• Added the computeMatrixOperations tools, which can be used to sort/reorder/subset/filter/combine the output of computeMatrix.
• computeMatrix --sortRegions has a new keep option, which is the default. This mimics the behavior in deepTools prior to 2.3.0 where the output order matched the input order. This is, of course, a bit slower, so if the order doesn't matter then use no.
• Fixed issue #435, where plotHeatmap --sortRegions region_length would crash with an error.
• Output bedGraph files are now sorted (#439).
• Values stored in bedGraph files (and therefore placed into bigWig files) now use python's "general" format with 6 digits of precision. This tends to produce slightly larger files, but with less loss for values near 0 (see #438).
• Corrected how computeGCBias determines the lambda parameter, which should only really affect very atypical experiments (i.e., correctGCBias would have crashed is this greatly affected you).