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)
class FileType:
MAF, VCF, HLA, GENE_EXP = range(0, 4)

Just a vanilla enum, no values like .hla are defined. Held off on that because gene expression files aren't necessarily defined by their extension (e.g. "blah.gene.normalized"). I initially was avoiding conditioning by just passing around different file_read funcitons (read_hla, etc.), which I prefer but felt non-Pythonic.