Drep

Fixed
- prodigal now multithreads the correct amount
- compare_wf double-printing issue
- --SkipMash now works

Changed
- default checkM method is now lineage_wf in dereplicate_wf, filter, and choose
- pyenv now reverences non-anaconda in the documentation and error messages
- default min length in now 50,000

Added
- more thorough testing (though still not nearly enough)
- log now contains the exact command run

Fixed
- Mash sketch size argument actually works now

Fixed
- Fixed analyze to produce non-ugly plots

Added
- Can now change the method of calculating coverage with ANIn
- Added TODO

Fixed
- Bug that caused the program to crash when looking for Mash
- Lots of typos (in documentation and program help)

Changed
- Fixed some typos in documentation
- Added bioRxiv link in documentation

Fixed
- Edited matplotlib to make text that can be edited by illustrator