Uropa

- Rearranged package structure towards a full Pypi packages
- Renamed summary.R to utils/uropa_summary.R
- Renamed reformat_output.R to utils/uropa_reformat_output.R
- Reflected changes in documentation

- Added an UpSetR plot to summary.R to cancel the need for Vennerable R package
- Added proper help to uropa2gtf.R script
- Reflected changes in documentations

- Added proper help for axillary R scripts (exit code 0)
- Made call to reformat_output.R multi-threaded
- Cleaned some code, added citation

- Bug fix for possible older versions of GNU sort, the order of results may have changed now
- Added protection against empty GTF files
- Clarified Tabix warning messages with proper genome coordinates.

- Introduced parameter -p/--prefix, replaces -o/--output
- Replaced parameter --no-comment by --add-comments
- Renamed output files to prefix_allhits.txt, prefix_finalhits.txt and prefix_besthits.txt
- Updated summary script for new gridExtra requirements (rows=NULL instead of show.rownames=FALSE)
- Fixed bug in log file handling
- Fixed bug in internals features, now works for distances larger than default distance
- Removed summary config after usage, removed split_peaks subdirectory in case of multi threading

- Fixed bug for log files in subdirectories
- Added new parameter --no-comments to skip comments in output tables
- Moved reduced annotation to output folder
- Minor changes in parameter descriptions