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. 
We added support for too many formats initially, and I'm trying to pare things down the ones we actually use. FASTA files require some auxiliary information to work with the rest of the code (which mutation generated each sequence). We should eventually come up with a format for stuffing all that into FASTA info lines, but seems very low priority.