Instrain

- Change genome_wide to include sums of SNPs
- GeneProfile now reports reference SNPs as well in terms of N and S
- Many updates to plotting function (listed below)
- The debug option will now produce a stack track for failed plots
- Plot basename now included in figure creation
- You can now plot only genomes meeting a breadth requirement
- You can now specify which genomes to plot
- Fixed bug preventing plots 2 and 7 from being made in a lot of cases
- Plot 4 now plots only freq > 0.5 and a set 50 bins

- Change genome_wide to account for ANI, popANI, and conANI

- Big changes to inStrain compare (stores SNVprofiles as globals; calculates popANI and con_ANI always; big changes to how popANI is calculated)

- Update to try and get the Null model properly installed

- Plot 9 displays titles now
- Fixed some of the test data; was previously on a non-mm level
- Set a maximum figure size of 100 inches on the scaffold inspection plot
- Update the docs for example_output
- Edit the GitHub README

- InStain only yells at you if the minor version is different
- Add microdiversity in addition to clonality for user-facing output
- Change the name "morphia" to "allele_count"
- Bugfix for geneProfile on lien 92 related to "if scaffold not in covTs"
- Move calculate_null.py into the helper_scripts
- Delete "R_scripts" and "notebooks" folders
- Delete combine_samples.py
- Change the name of combined_null1000000.txt to NullModel.txt
- Changes to internals of calculate_null.py; add parameters so that others could change it if they want to as well
- Change the default NullModel to go up to 10,000 coverage, with X bootstraps
- Add plots 8 and 9
- Small changes to ReadComparer to try and reduce RAM usage by decreasing the amount of SNPtable stored
- Plot 10 can now be made
- Add dRep to required list
- Change the null model to be mutlithreaded
- NullModel.txt has 1,000,000 bootstraps
- Fixed a bug in making plot2