getting read to work on CLIP_analysis, added comments where I could
wrote basic tests realized that I have no idea what I'm doing
did some basic refactoring and testing on clip analysis.  (got an allup test to partially work).  About to make sweeping changes to plotting.  Need a checkpoint
refactored majority of display code, still need to add back in z-score display and phastcons stuff
added flag to remove global transcriptome filtering, global-cutoff
Merge branch 'dev' of https://github.com/YeoLab/clipper into gtf_conversion
Merge branch 'master' of https://github.com/YeoLab/clipper into gtf_conversion
deleted foo
fixed gzip bug and added an additional test
added kmerdiff (broken) and an ignore file to clean up annoying checkins
Merge branch 'dev' of https://github.com/YeoLab/clipper into dev
cleaned up tests
FDR threshold is now the min(gene_threshold, SLoP_threshold)
added tests to verify that transcriptome wide filter is working