Pydnase

Latest version: v0.3.0

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0.3.0

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* 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

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* 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

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* 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

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* BUG: Update author’s contact details

0.2.3

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* 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

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* BUG: Fix error in ``wellington_bootstrap.py``

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