Fixed terrible threading problems, whereby there was no way to quit from
the program.

Control - C handling was an issuse,

The problem stemmed from having the threads exit with out notifying the
queue they had actually done the work.
Fixed queue based scheduler to make it work properly
Made the pipeline preserve the original VCF file before all the
filtering and shunting has occurred
Merge branch 'master' into fix_threading
Changed standard run slightly
Reset the state at which to switch to running the entire
selection_pipeline in parallel
Merge branch 'fix_threading' of github.com:smilefreak/selectionTools

Conflicts:
	selection_pipeline/multipipeline.py
Fixed problems with aa_annotate and various other bugs
Merge branch 'master' of github.com:smilefreak/selectionTools
Fixed aa annotate