Added beagle to the pipeline
Removed bug with using beagle for the analysis
beagle _new
Set a more sensible default for HWE settings
Fixed installation to work with mac os x !
Found some people added beagle to the analysis
Added end of pipeline run message to be printed to stdout
Removed shapeit from the analysis
Removed shapeit from the pipeline
Merge branch 'add_beagle' of github.com:smilefreak/selectionTools into add_beagle
Made the pipeline not delete the config file when the config file is in
one of the processing folders
Changed install to remove shapeit files
Added tajima's D
Merging changes for tajima's D MAC OSX
Merge branch 'add_beagle' of github.com:smilefreak/selectionTools into add_beagle

Conflicts:
	selection_pipeline/standard_run.py
Made some changes getting ready to work with genetic maps interpolate
and integrating said results into the current incantation of the
pipeline
Moved the genetic map to it's own section of the config file
Started integrating a genetic map into the pipeline,

also enabled the usage of REHH with a genetic map which took
some fiddling to get working.
Updated the manual to reflect the changes, Everything should be A OK
Made systematic changes to the pipeline, testing multicore IHH to see if
it is working when using linear interpolation