0.3.0

0.3.0 - 2018-04-01

• IMPORTANT: Default number of threads in wellington_footprints.py now set to 1 - set to 0 to use all cores
• BUGFIX: Fix Cython code for latest Cython
• BUGFIX: Logic fixes to underlying Wellington C code (@dpryan79)
• BUGFIX: Shebangs added to python scripts (@dpryan79)
• BUGFIX: Fix ability to compare GenomicInterval objects in python3 (@dpryan79)

0.2.6

0.2.6 - 2018-01-27

• ENHANCEMENT: License changed to MIT
• BUGFIX: Scripts should now all work for Python 3
• BUGFIX: Empty lines in BED files are now ignored
• BUGFIX: Fix issue with passing values to the "-pv" argument on wellington_footprints.py

0.2.5

0.2.5 - 2016-07-23

• IMPORTANT: Python 2.6 and 3.2 support dropped. 2.7, 3.3, 3.4, and 3.5 are where it's at.
• BUG: pyDNase now ignores unmapped reads in the BAM input file. NOTE: Will not ignore secondary alignments in paired reads. Filter these out beforehand if you need this behaviour for the timebeing.
• BUG: Fix dnase_bias_estimator.py script arguments.
• BUG: Fix frd_limit flag not being able to be set to 0 in wellington_footprints.py and wellington_bootstrap.py.

0.2.4 - 2016-05-30

BUG: Update author’s contact details

0.2.3

0.2.3 - 2016-01-17

• BUG: Fix error in wellington_bootstrap.py which caused no output to be written to disk (thanks to Duy Pham for reporting)

0.2.2

0.2.2 - 2015-12-26

• BUG: Fix error in wellington_bootstrap.py

0.2.1

0.2.1 - 2015-12-25

• ENHANCEMENT: ATAC-seq mode for wellington_bootstrap.py

0.2.0

0.2.0 - 2015-12-18

• 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 for full documentation)
• FEATURE: Calculate ∆DHS (He et al. 2012) 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.

0.1.5

0.1.5

pyDNase 0.1.2

Fix issue where BED intervals with chromosome names not starting with "c" were silently being ignored (reported by Aaron Hardin)
Fix clint dependency issue (no longer requires custom version of clint)
Fix spelling error in CHANGES