Analyze cohort

Added `analyze_cohort.py` which summarizes a directory of MAF/VCF files by associating each filename with the number of immunogenic mutations. Also renamed cancer\_pipeline to mutation_report and deleted unused files. 
Am I being overly permissive in allowing either newlines or commas as seps? I'm anticipating eventually John F or someone else using this code who might need the rules to be forgiving.