* Modified how normalization is done when filtering is used. Previously, the filtering wasn't taken into account when computing the total number of alignments. That is now being done. Note that this uses sampling and will try to sample at least 100000 alignments and see what fraction of them are filtered. The total number of aligned reads is then scaled accordingly (309).
* Modified how normalization is done when a blacklist is used. Previously, the number of alignments overlapping a blacklisted region was subtracted from the total number of alignments in the file. This decreased things a bit too much, since only alignments falling completely within a blacklisted region are actually excluded completely (312).
* BED12 and GTF files can now be used as input (issue 71). Additionally, multiBamSummary, multiBigwigSummary and computeMatrix now have a --metagene option, which allows summarization over concatenated exons, rather than include introns as well (this has always been the default). This was issue 76.
* Read extension is handled more accurately, such that if a read originates outside of a bin or BED/GTF region that it will typically be included if the --extendReads option is used and the extension would put it in a given bin/region.
* deepTools now uses a custom interval-tree implementation that allows including metadata, such as gene/transcript IDs, along with intervals. For those interested, the code for this available separately (https://github.com/dpryan79/deeptools_intervals) with the original C-only implementation here: https://github.com/dpryan79/libGTF.
* The API for the countReadsPerBin, getScorePerBigWigBin, and mapReduce modules has changed slightly (this was needed to support the --metagene option). Anyone using these in their own programs is encouraged to look at the modified API before upgrading.
* Added the `plotEnrichment` function (this was issue 329).
* There is now a `subsetMatrix` script available that can be used to subset the output of computeMatrix. This is useful for preparing plots that only contain a subset of samples/region groups. Note that this isn't installed by default.
* The Galaxy wrappers were updated to include the ability to exclude blacklisted regions.
* Most functions (both at the command line and within Galaxy) that process BAM files can now filter by fragment length (--minFragmentLength and --maxFragmentLength). By default there's no filtering performed. The primary purpose of this is to facilitate ATACseq analysis, where fragment length determines whether one is processing mono-/di-/poly-nucleosome fragments. This was issue 336.
* bamPEFragmentSize now has --logScale and --maxFragmentLength options, which allow you to plot frequencies on the log scale and set the max plotted fragment length, respectively. This was issue 337.
* --blackListFileName now accepts multiple files.
* bamPEFragmentSize now supports multiple input files.
* If the sequence has been removed from BAM files, SE reads no longer cause an error in bamCoverage if --normalizeTo1x is specified. In general, the code that looks at read length now checks the CIGAR string if there's no sequence available in a BAM file (for both PE and SE datasets). This was issue 369.
* bamCoverage now respects the --filterRNAstrand option when computing scaling factors. This was issue 353.
* computeMatrix and plotHeatmap can now sort using only a subset of samples
* There is now an --Offset option to bamCoverage, which allows having the signal at a single base. This is useful for things like RiboSeq or GROseq, where the goal is to get focal peaks at single bases/codons/etc.
* The --MNase option to `bamCoverage` now respects --minFragmentLength and --maxFragmentLength, with defaults set to 130 and 200.