Updates to README.md
Formatting....
Merge remote-tracking branch 'origin/develop' into refactor
converted to new structure
fixed typo
remove base since we are not using it yet
remove splitter
fixed issues from assembler rename
fixed config issues
initial refactor giving same results as develop
rename Extentions to contrib
remove print probes
added config file command line option and fixed key error in config
updated help description for config
update setup.py for new structure, move some of run in process runner into new function and rename ref_q to job_q
join expects string
ignore comments in samples, add check for addRun exe.
Merge remote-tracking branch 'origin/refactor' into develop

Conflicts:
	ARC/__init__.py
re-add header for cDNA, and checks for equal number of reads in PE.