2.4.3

• Fixed incorrect label ordering in the plotCorrelation command with the --outFileCorMatrix options.
• Fixed bug #491, which involved python 3 and bamCoverage.

2.4.2

• Fixed an issue where computeMatrix reference-point --referencePoint center would break if 1-base regions were used. This was bug #456.
• plotCorrelation with --outFileCorMatrix now works with --labels again (thanks to @sklasfeld for supplying the patch).
• bigwigCompare and bamCompare can now return the average (mean) of two input files (issue #467).

2.4.1

• Setting --zMin to the same value as --zMax, whether intentionally or because the --zMax value computed by deepTools happens to be now larger than the desired value, will result in the maximum value in the dataset being used (internally, --zMax gets set to None).
• Scale factor is now set to 1 in bamCoverage if no normalization is used. The fact that this wasn't being done previously was a bug.
• Fixed a bug (#451) affecting BED files with a deepTools_group column that caused a problem with --sortRegions keep in computeMatrix.
• Fixed a bug where some matrices produced with computeMatrixOperations cbind would result in the right-most samples sometimes getting squished due to having ticks outside of their graph bounds. Ticks are now scaled if they don't match the data range (issue #452).
• In plotFingerprint, the number of reads per-bin are no longer used. Instead, the sum of the per-base coverage (or signal if bigWig input is used) is used. This leads to more similar metrics produced by us and others regarding things like Jensen-Shannon metrics. For those just interested in the plots, there's little effective change here.

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).

2.3.6

• multiBamSummary will now not automatically append .npz to the output file name if it's not present. This was bug #436
• Fixed a bug with plotHeatmap where --yMin and --yMax didn't work

2.3.5

• Various Galaxy wrapper fixes (e.g., issue #415 and #417)
• Fixed issue #413, wherein the --nanAfterEnd option sometimes causes computeMatrix to throw an error.
• Fixed issue #416, wherein --outRawCounts in multiBamSummary and multiBigwigSummary would cause an error if python3 was being used.

2.3.4

• Fixed bug #405, which dealt with the SES normalization in bamCompare (it was producing an error and terminating the program).
• Fixed bug #407, which dealt with multiBamSummary or multiBigwigSummary bins and saving the raw data. This was causing an error and the program to terminate.

2.3.3

• Fixed a bug wherein proper pairs where being incorrectly called improper pairs, thereby causing slightly incorrect read extension.

2.3.2

• The deeptoolsinterval module was modified to speed up plotEnrichment, which was taking forever to finish.

2.3.1

• This release has no real code changes, the 2.3.0 release on pypi was missing files.