Added gene expression filtering using RNASeq data

Main piece of logic is at Line 315: "if genes_expressed:"

Style changes to be merged first as #121, before merging this PR.

Other changes include:

- Some debugging arguments
- Refactoring some logic out of find_hla, so it can be used for HLA and gene expression files
- splitext_permissive so that we can use .hla.txt (for example)

Sample run on TCGA-61-2113 (OV, RNASeq v1):

TCGA-61-2113: # mutations 38 (323 epitopes), # mutations with ligands 8 (8 epitopes), # immunogenic mutations 7 (7 epitopes), # immunogenic mutations with gene expression 6 (6 epitopes)
I think I like the file_read functions a little more than a flag. Then you encapsulate the higher order base function by making collect_hla_files and collect_gene_files. But it's not a big deal.