Refactoring of lib.fileio.auto_open to work with subprocess (#266) (#267)

* Deprecate pipes and use subprocess instead.

* Class structure behind fileio.auto_open with retained backwards compatibility with pairtools v1.1.3 and before. Extensive documentation of the fileio. 

* New feature: check bgzip version and skip if the version is too old to support multithreading. 

* Minor updates: update _logging.py , improve dedup notebook (OSF sample added), scaling notebook updated, 

* Checks: pairtools walkthrough and other examples checked for compatibility. distiller-nf and pytest tests are all valid.

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Co-authored-by: @Reovirus @agalitsyna

Reviewed by: @golobor (Open2C meeting) @Phlya

Author: Reovirus