charlesfoster

Hello again, I've been revisiting `mmseqs` again for taxonomic assignment, and unwittingly ran into this problem again before finding my own Github issue (the circle of life!). I was just...

I've just come across this same query, and, from what I can tell, `genomecov` does use non-primary alignments. To figure this out, I compared it to calculations from `mosdepth`. ```...

Great, thanks. I'll follow along :) In the meantime I've just got the following hacky code in my Nextflow script which does the job: ``` ## modify the file headers...