Atropos

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* Fix 87 - Python 3.8 compatibility, time.clock removed

* Set minimum Python version to 3.4.5
* Fixed 86 - no trimming performed for single-end BAM file

* Documentation fixes (79)
* Fix for index error when running `detect` command (80)

* Added long options for paired adapter parameters.

* Fix 74: Make pysam open SAM/BAM files with check_sq=False by default
* Fixed setup.py to correctly include README for PyPI.

* Fix 68: Error when using insert aligner with adapters of different lengths

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