added ability to generate frea files from gtf.  Need to make changes to AS structure processing before actually including though
finished fixing argunments and testing for the switch to genomic_locations gtf files
Merge branch 'dev' of https://github.com/YeoLab/clipper into dev
fixed bug in calculate phastcons and added option for different types of analysis in call_peak (not doing anything yet)
fixed small crash bug with kmers
refacotred some AS_structure files so I can work with them without having to change matplotlib settings
fixed bug where automaticall generated bed files would not be placed in assigned directory
added bonferroni correction as an option to filter outputs
text cleanup
Merge branch 'dev' of github.com:YeoLab/clipper into dev
bugfix in kmerdiff.py
fixed z-scores and motifs not displaying in clip analysis
fixed various display issues in CLIP_Analysis
fixed kmer diff outputting to stdout when it shouldn't
fixed various display issues with CLIP_Analysis, it should work as was originally implemented (but more robustly
fixed count genomic regions to not have regions file
Merge branch 'dev' of https://github.com/YeoLab/clipper into dev
added ability to output metrics file, included fraction of reads in peaks staststic
removed trackline creation from clipper output, it screws up to many downstream analysies.  Trackline will get added in pipeline, not before.
added in some missing test files, also fixed bonferoni correction so as to not have p-value go above one, finally removed trackline from bedtool output.  Will add in this information later