v0.2.5

[ktmeaton]

1. Separate mugration notebook into model and plot.
2. Add a heatmap test, output to misc.
3. Create a new rule to generate locus coverage.
4. Remove output directory of eager rule.
5. Make a list of target genes
   • pPCP1 - pla (AL109969,6665,7603,pla)
6. Hard code target genes into ref locus bed
7. Move ref locus bed to reference
8. Create gene by gene coverage.
9. Analyze both coverage and depth of loci.
10. Compare gene to plasmid coverage (pla, pPCP1)
11. Apply a coverage filter for pPCP1 plasmid.
12. Add locus coverage info to nexus tree.
13. Created spreadmaps for branch major.