Instrain

- Update to genome_wide calculations on the mm-level

- Add the "plot" module

- Add the "genome_wide" module

- Compare is now stored in an SNVprofile object as well
- The log of compare is stored in the log folder
- The log of profile is stored in the log folder

- Add a README to the raw_data folder
- Add mean_microdiversity and median_microdiversity to the scaffold table in addition to clonality
- Scaffolds with no clonality are np.nan, not 0
- Change the name from ANI to popANI in ReadComparer
- GeneProfile now stores the SNP mutation types in the output
- The name of the IS is now stored in front of everything in the output folder
- GeneProfile now correctly identifies genes as being incomplete or not

- Whole new way of running inStrain is born- everything under the same parser