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* FEATURE: Differential Footprinting between treatment and control (``wellington_bootstrap.py``)
* FEATURE: Estimate 6-mer bias cleavage (``dnase_bias_estimator.py``)
* FEATURE: ATAC-seq compatability! (pass -A to most of the scripts to enable ATAC-seq read shifting for the transposase staggered integration)
* FEATURE: Preliminary DNase I cleavage bias correction in ``dnase_average_profile.py`` and ``dnase_to_javatreeview.py`` (see `here <http://pythonhosted.org/pyDNase/biascorrecting.html>`__ for full documentation)
* FEATURE: Calculate ∆DHS `(He et al. 2012) <http://www.ncbi.nlm.nih.gov/pubmed/22508765>`__ scores between two DNase-seq runs (``dnase_ddhs_scorer.py``)
* FEATURE: Annotate BED file number of cuts in each region (``dnase_cut_counter.py``)
* ENHANCEMENT: DNase-seq footprinting tutorial :)
* ENHANCEMENT: In the interests of performance, ``BAMHandler`` no longer returns NumPy arrays, just lists.
* ENHANCEMENT: ``wellington_footprints.py`` is now multithreaded (woo) - performance roughly scales linearly with number of CPUs.
* ENHANCEMENT: The ``Footprinting`` module has been refactored to allow for multithreading - those using the Wellington API directly take note of the changes.
* ENHANCEMENT: Everything is faster! More cythonised code.