Merge pull request #114 from hammerlab/string_distance

Tabs to spaces, and adding self.data_path = data_path
added cohort analysis, renamed cancer_pipeline to mutation_report
print summary of immunogenic mutations at the end of script
Change MutationInfo to GeneMutationInfo
show peptide, not gene, mutation info on html report
code review fixes
Merge pull request #115 from hammerlab/analyze_cohort

Analyze cohort
First draft of a PMBEC class based on iskandr/mhcpred/pmbec.py
Fixing PMBEC distance so that distance(A, A) == 0
Adding positional weights
Merge branch 'string_distance' of https://github.com/hammerlab/immuno into string_distance