ideas for major feature additions in 0.3.0

[nellore]

• Resolve multimapping reads in a way that makes the most sense for downstream analyses. (How? Push coverage distribution toward more uniformity like MMR?)
• Add option to run job flow with Spark on EMR
• Permit automated sample clustering for collective analysis and report clusters?
• Add more normalization methods
• Play even nicer with derfinder; compute region matrix?
• Investigate --bind-to-socket in MPI to constrain processor usage on cluster
• Code robustness to losing and gaining ipengines in emr_simulator.py