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.

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.