* Add flexibility to allow for additional MetaPhlAn output column.
* Split "--identity-threshold" into two options, one for each search type with defaults of 0 (nucleotide) and 80/50 (translated).
* Update diamond default options to "--id 80.0 --top 1" for UniRef90 runs and "--id 50.0 --top 1" for UniRef50 runs.
* Updated databases to use the latest ChocoPhlAn and corresponding UniRef50/90 (release 01/2019).
* Added diamond options.
* Added bowtie2 options.
* Added gene based filtering to nucleotide search using the same method as translated search. To revert back to prior nucleotide filtering mode, run with the options "--nucleotide-subject-coverage-threshold 0 --nucleotide-query-coverage-threshold 0".
* Add flexibility to MetaPhlAn version check to allow for warning messages for numpy and biom-format.