PEP 8 plus starting using python OO properly
Fixed constructor calls from standard run
to the parent constructor in run_pipeline
Deleted byte code compiled python filen
Added proper oo calls.
Moved core scripts back to core scripts folder
Deleted reference to nesi
Fixing bugs in cores scripts and aa_annotate regarding phased vcf file
Mostly working with updates only missing the updates to subprocess to
stop deadlock on the master branch.
Merge branch 'oo'

Conflicts:
	selection_pipeline/standard_run.py
	selection_pipeline/standard_run_utilities.py