- 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