Pararead

Fixed
- Updated Python version
- Cleaned and lint the code

Changed
- Use command callability checker from `ubiquerg`.
- Moved to logmuse, removing the logging functions from pararead

Fixed
- Fixed bug with example that prevented it from working on multiple cores

- Made compatible with python 3

Added
- Added `retain_temp` argument that is useful for debugging.
- Added modified version of read counting example to demonstrate logging.

Changed
- Updated the CLI for logging options

Changed
- Updated packaging and documentation for release on pypi.

Changed
- A `ParaReadProcessor`'s `__call__` function is no longer applied to any
chromosome that's empty (i.e., to which no reads mapped). Instead, an action
(`empty_action`, which may be overridden) is taken for such a chromosome.
This frees an implementor of `ParaReadProcessor` from the need to worry about
empty chromosomes while allowing the flexibility for custom action in that case.