Add collapse taxonomy/combine outputs features

[microbemarsh]

Possible Enhancement

I know you're prob just a little busy but for interpreting the results at higher taxonomic levels down the line these might be useful to add:

https://github.com/treangenlab/emu?tab=readme-ov-file#collapse-taxonomy

https://github.com/treangenlab/emu?tab=readme-ov-file#combine-outputs

[nsapoval]

I believe the collapse_ranks function (lines 756-776) already does that. The corresponding CLI flag is -r, --rank and it defaults to species. However, you should be able to specify genus or any other rank that is part of the full output as an option.

Let me know if this works or if you encounter any bugs while trying it out. In the meantime, I'll work on writing the usage section of README to cover all of the flags currently supported.

[microbemarsh]

Ah sorry, I see now. I guess just a combine-outputs function would be useful too if running multiple samples together but users could always do that part themselves

[nsapoval]

Ah I see what you mean. I'll work on this soon.