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Fix issue with strand_specific code #2
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parmap 1.5.0 introduced support for passing keyword arguments to mapped functions, as keyword arguments were not supported before. The drawback of this new feature is that a consistent naming of parmap arguments is needed in order to prevent conflicts between parmap arguments and user-defined arguments. The new parmap convention is to prefix all its arguments with "pm_" (for parmap) as documented http://parmap.readthedocs.io/en/latest/ This commit updates the cll-chromatin parmap calls to use the new API, removing the deprecation warnings that appear with parmap==1.5.1 (the parmap version used).
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Hi,
As the parmap author I have been contacting parmap users to make sure they can smoothly update to the minor API changes I had to make in
parmap==1.5.0. This pull request updates your code to reflect those changes. Basically I had to replaceparallel=Truewithpm_parallel=True. It has been so far a very smooth upgrade with no issues in any other parmap user.Unfortunately, I have found an issue in your usage of parmap that may have lead to some incorrect results. Until parmap 1.5.0,
parmap.mapsupported multiple positional arguments, but not keyword arguments. This was stated in the README. However, you were usingparmapand trying to pass thestrand_specific=keyword argument in this line of code. I am sorry to say that this keyword argument was never passed to the underlyingcoverage_singlefunction, and therefore the defaultstrand_specific=Falsewas always used.If you want to check the impact of this bug on your results, please make sure you have the latest parmap version installed (which does support keyword arguments, you can use
pip install -U parmap) and run your code again, once you have accepted this pull request. I hope for the best and that the impact is small.Best,
Sergio