fixed display where stop codons were improperly listed as start codons
small refactor / cleanup of old code in get_features
added quick hack to find the exon (or region number) of bound RBP
updated region distributions for hg19 and mm9 to be bug free
Merge branch 'master' of https://github.com/YeoLab/clipper
significantly spead up count total reads function
added in fail fast error if there aren't a lot of peaks, may want to remove later
Merge branch 'master' of https://github.com/YeoLab/clipper
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added Null default to constructor so it doesn't fail when pulling the args out to use in a notebook
added flag to infer gene and thick / think peak sites if not defined by the algorithm.
made it so clip analysis failed quickly on no reads
updated clipper to use norm residuals again, seeing if we can get better peaks that way
Updated plotting functionality to output svg and make text editable
modified peak calling to use optomize_scaler and it looks like it works, pusing to tscc for large scale tests
did stuffs (tweaked tightness to call more smaller peaks)
standardized paramater passing for clipper, and cleaned up some typos and spelling errors
call peak modified to use minimze scalar
removed lots of unnessessary testing files
swapped min and max for superlocal FDR cutoff.