Bedboss

Added

- Added open_chromatin plot back into processing.
- Added gtrs dependency, that calculates gc content.
- Added skipper that automatically skips samples in pep that were already processed.
- Added lite functionality to main functions that allows to run uploading without using any heavy processing.
- Added function that will reprocess files, if they were unprocessed in the bedbase.
- Added function that predicts genome if genome wasn't provided.

Fixes
- Important speed improvements.
- Improved requirements checker.
- Minor bug fixes.

Added
- Standardization of peps using bedbase bedms schema
- Reference validator module

Fixed
- Pipeline failures (due to pipeline manager)
- Failure in cleaning temp files

Added
- Added bbuploader (GEO uploader)

Added
- Added classifier
- Added create universe uploader
- Added tokenization and token uploader

Changes
- Updated efficiency of CLI help

Changed
- small naming tweaks

Added
- added requirement check to cli

Changed
- moved all uploading functionality to the `bbconf` package

Added
- added commands for indexing bedfiles
- added commands for deleting bedfiles and bedsets